RSS Feed Microbiology

Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis.

Microbiology. 2010 Feb 4;

Authors: Morinaga T, Ashida H, Yoshida KI

scyllo-Inositol (SI) is a stereoisomer of inositol whose catabolism has not been characterized in bacteria. We found that Bacillus subtilis 168 was able to grow using SI as its sole carbon source and that this growth was dependent on the functional iol operon for catabolism of myo-inositol (MI; another inositol isomer, which is abundant in nature). Previous studies elucidated the MI catabolic pathway in B. subtilis comprising multiple stepwise reactions catalyzed by a series of Iol enzymes. The first step of the pathway is known to convert MI into scyllo-inosose (SIS) and involves the MI dehydrogenase IolG. Since IolG does not act on SI, we suspected that there could be another enzyme converting SI into SIS, namely an SI dehydrogenase. Within the whole genome, seven genes paralogous to iolG have been identified and two of these, iolX and iolW (formerly known as yisS and yvaA, respectively), were selected as candidate genes for the putative SI dehydrogenase since they were both prominently expressed when B. subtilis was grown on SI medium. iolX and iolW were cloned in Escherichia coli and both were shown to encode a functional enzyme, revealing the two distinct SI dehydrogenases in B. subtilis. Since inactivation of iolX impaired the growth using SI as the carbon source, IolX was identified as a catabolic enzyme required for SI catabolism and it was NAD+ dependent. The physiological role of iolW remains unclear, but it may be capable of producing SI from SIS with NADPH oxidation.

PMID: 20133360 [PubMed - as supplied by publisher]

Diversity of CRISPR loci in Escherichia coli.

Microbiology. 2010 Feb 4;

Authors: Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ

CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species to further contribute to the understanding of the CRISPR mode of action had not yet been addressed. Here we describe two CRISPR/CAS systems found in E. coli following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preference and CRISPR relevance for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.

PMID: 20133361 [PubMed - as supplied by publisher]

An archaeal order with multiple minichromosome maintenance genes.

Microbiology. 2010 Feb 4;

Authors: Walters AD, Chong JP

In eukaryotes a complex of six highly related minichromosome maintenance (MCM) proteins is believed to function as the replicative helicase. Until recently, systems for exploring the molecular mechanisms underlying eukaryotic MCM function have been biochemically intractable. To overcome this, molecular studies of MCM function have been carried out using MCM homologues from the archaea. Archaeal MCM systems studied to date possess a single functional MCM, which forms a homohexameric complex displaying DNA binding, ATPase and helicase activities. We have identified an archaeal order that possess multiple MCM homologues. BLAST searches of available Methanococcales genomes reveal that members of this order possess between two and eight MCM homologues. Phylogenetic analysis suggests an ancient duplication in the Methanococcales gave rise to two major groups of MCMs. One group contains Methanococcus maripaludis S2 McmD and possesses a conserved C-terminal insert similar to one observed in eukaryotic MCM3, while the other group contains McmA, B and C. Analysis of the genome context of MCMs in the latter group indicates these genes could have arisen from phage-mediated events. When co-expressed in E. coli the four MCMs from M. maripaludis co-purify, indicating the formation of heteromeric complexes in vitro. The presence of homologues from both groups in all Methanococcales indicates that there could be functionally important differences between these proteins and that Methanococcales MCMs may therefore provide an interesting additional model for eukaryotic MCM function.

PMID: 20133362 [PubMed - as supplied by publisher]

Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase.

Microbiology. 2010 Feb 4;

Authors: Krejcik Z, Hollemeyer K, Smits TH, Cook AM

Bacterial generation of isethionate (2-hydroxyethanesulfonate) from taurine (2-aminoethanesulfonate) by anaerobic gut bacteria was established in 1980. That phenomenon in pure culture was recognized as a pathway of assimilation of taurine-nitrogen. Based on the latter work, we predicted from genome-sequence data that the marine gammaproteobacterium Chromohalobacter salexigens DSM 3043 would exhibit this trait. Quantitative conversion of taurine to isethionate, identified by mass spectrometry, was confirmed, and the taurine-nitrogen was recovered as cell material. An eight-gene cluster was predicted to encode the inducible vectorial, scalar and regulatory enzymes involved, some of which were known from other taurine pathways. The genes (Csal_0153-Csal_0156) encoding a putative ATP-binding cassette transporter for taurine (TauAB1B2C) were shown to be inducibly transcribed by reverse transcription (RT-) PCR. An inducible taurine:2-oxoglutarate aminotransferase (Toa) [EC 2.6.1.55] was found (Csal_0158); the reaction yielded glutamate and sulfoacetaldehyde. The sulfoacetaldehyde was reduced to isethionate by NADPH-dependent sulfoacetaldehyde reductase (IsfD), which was attributed to the short-chain alcohol dehydrogenase superfamily. The 27-kDa protein (SDS-PAGE) was identified by peptide-mass fingerprinting as the gene product of Csal_0161. The putative exporter of isethionate (IsfE) was encoded by Csal_0160; isfE was inducibly transcribed (RT-PCR). The presumed transcriptional regulator, TauR (Csal_0157), may autoregulate its own expression, typical of GntR-type regulators. Similar gene clusters were found in several marine and terrestrial gammaproteobacteria, which, in the gut canal, could be the source of not only mammalian, but also arachnid and cephalopod isethionate.

PMID: 20133363 [PubMed - as supplied by publisher]

Monash University biochemists have found a critical piece in the evolutionary puzzle that explains how life on Earth evolved millions of centuries ago. The team, from the School of Biomedical Sciences, has described the process by which bacteria developed into more complex cells and found this crucial step happened much earlier in the evolutionary timeline than previously thought...

Within a virus's tiny exterior is a store of energy waiting to be unleashed. When the virus encounters a host cell, this pent-up energy is released, propelling the viral DNA into the cell and turning it into a virus factory...

Conclusions: The expression of genes encoding proteins involved in the beta-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways. (Source: BMC Microbiology - Latest articles)

Menon Santosh, Pai Prathamesh, Sengar Manju, Aggarwal J P, Kane Shubhada V

Indian Journal of Pathology and Microbiology 2010 53(1):28-34

Primary sinonasal tumors with neuroendocrine differentiation (SCND) are uncommon tumors with considerable overlap of histological features. Based on their neuroendocrine differentiation they can be sub categorized into sinonasal undifferentiated carcinoma (SNUC), sinonasal neuroendocrine carcinoma (SNEC), esthesioneuroblastoma (ENB) and small cell carcinoma (SmCC). The natural history and biological behavior varies in this group of tumors. Hence the histo-morphological diagnosis coupled with grading/staging is important for the prognostication of these tumors. <b> Aim</b> : To study the clinicopathological characteristics of sinonasal neuroendocrine malignancies at our institute.<b> Material and Methods</b> : We searched our institute's pathology database for the period from 2002 to 2007, for the four subcategories of sinonasal tumors with neuroendocrine differentiation. Morphological and immunohistochemical features were studied and, grading, staging was done in accordance with standard criteria. The clinical treatment and follow- up data were retrieved from the case files in available cases. <b> Results</b> : A total of 37 cases were retrieved from our database which include 14 cases of SNUC, 14 cases of ENB and nine cases of SNEC. The cases of SNUC were immunopositive for cytokeratin, epithelial membrane antigen and weakly for neuron-specific enolase. SNEC showed strong reactivity with epithelial and neuroendocrine markers whereas ENB demonstrated immunoreactivity to synaptophysisn and chromogranin strongly, with weak to negative expression of epithelial markers. All cases of SNUC and SNEC were of high grade and stage whereas 50% of ENB cases were of grade II but high stage tumors. Most of the SNUC and SNEC patients had been treated with multimodality treatment regimens including upfront chemotherapy followed by surgery and loco- regional radiation. In contrast, ENB patients had undergone surgical extirpation followed by radiation therapy in majority of cases. With limited follow-up data, it was observed that four out of five SNUC patients and three out of four SNEC patients developed either loco-regional (three of SNUC and two of SNEC) or distant metastasis (one patient each of SNUC and SNEC). ENB patients also had loco-regional recurrences (five out of seven patients) with a more protracted course but no distant metastases were observed during the follow up in available cases.<b> Conclusion</b> : Sino nasal tumors with neuroendocrine differentiation are a heterogenous group of tumors with overlapping histo-morphological features. They can be distinguished based on immunohistochemical characteristics. Pathological sub categorization is imperative for management and prognostication of these aggressive tumors.

Understanding that genes code for proteins and proteins function as enzymes is the foundation for basic genetics (dominance, phenotype) and molecular biology.

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Antisense transcription in gammaretroviruses as a mechanism of insertional activation of host genes.

J Virol. 2010 Feb 3;

Authors: Rasmussen MH, Ballarín-González B, Liu J, Lassen LB, Füchtbauer A, Füchtbauer EM, Nielsen AL, Pedersen FS

Transcription of retroviruses is initiated at the U3-R boundary in the integrated provirus and continues uni-directionally to produce genomic and messenger RNA products of positive polarity. Several studies have recently demonstrated the existence of naturally occurring protein-encoding transcripts of negative polarity in complex retroviruses. We report here on the identification of transcripts of negative polarity in simple murine leukemia virus (MLV). In T-cell and B-cell lymphomas induced by SL3-3 and Akv MLV, antisense transcripts initiated in the U3 region of the proviral 5' LTR and continued into the cellular proto-oncogenes Jdp2 and Bach2 to create chimeric transcripts consisting of viral and host sequence. The phenomenon was validated in vivo using a knock-in mouse model homozygous for a single LTR at a position known to activate Nras in B-cell lymphomas. 5' RACE analysis indicated a broad spectrum of initiation sites within the U3 of the 5' LTR. Our data for the first time show transcriptional activity of negative polarity initiating in the U3 region of simple retroviruses, and suggest a novel mechanism of insertional activation of host genes. Elucidation of the nature and potential regulatory role of 5' LTR antisense transcription will be relevant to the design of therapeutic vectors, and may contribute to the increasing recognition of pervasive eukaryotic transcription.

PMID: 20130045 [PubMed - as supplied by publisher]