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Brucella SRNA
Bacterial small RNAs (sRNA) are an important class of regulatory molecules in bacteria such as ''Brucella''. They are often bound to the chaperone protein Hfq, which allows them to interact with mRNA(s). In ''Brucella suis 1330'' RNA sequencing identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs. In ''Brucella melitensis'' eight novel sRNA genes were identified using bioinformatic and experimental approach. One of them BSR0602 was found to modulate the intracellular survival of ''B. melitensis''. In another large-scale deep sequencing study 1321 sRNAs were identified in ''B. melitensis.'' BSR0441 sRNA was further investigated in this study and shown to play role in the intracellular survival. sRNA BM-sr0117 from ''Brucella melitensis'' was identified and shown to be bound to and cleaved by Bm-RNase III. AbcR and AbcR2 (orthologs of SmrC15 and SmrC16) were studied '' B. abortus''. Seven novel sRNAs were validated and their interaction with a putative target seq ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacterial Small RNA
Bacterial small RNAs (bsRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including ''Escherichia coli'', the model pathogen ''Salmonella'', the nitrogen-fixing Alphaproteobacteria, alphaproteobacterium ''Sinorhizobium meliloti'', marine cyanobacteria, ''Francisella tularensis'' (the causative agent of tularaemia), ''Streptococcus pyogenes','' the pathogen ''Staphylococcus aureus'''','' and the plant pathogen ''Xanthomonas oryzae pathovar oryzae''. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure. Origin In the 1960s, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Brucella
''Brucella'' is a genus of Gram-negative bacteria, named after David Bruce (1855–1931). They are small (0.5 to 0.7 by 0.6 to 1.5 µm), non encapsulated, nonmotile, facultatively intracellular coccobacilli. ''Brucella'' spp. are the cause of brucellosis, which is a zoonosis transmitted by ingesting contaminated food (such as unpasteurized milk products), direct contact with an infected animal, or inhalation of aerosols. Transmission from human to human, for example, through sexual intercourse, or from mother to child, is exceedingly rare, but possible. Minimum infectious exposure is between 10 and 100 organisms. The different species of ''Brucella'' are genetically very similar, although each has a slightly different host specificity. Hence, the National Center for Biotechnology Information taxonomy includes most ''Brucella'' species under ''B. melitensis''. The many names of brucellosis include (human disease/animal disease): * Malta fever/Bang's disease * Undulant feve ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Deep Sequencing
Coverage (or depth) in DNA sequencing is the number of unique reads that include a given nucleotide in the reconstructed sequence. Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. Rationale Even though the sequencing accuracy for each individual nucleotide is very high, the very large number of nucleotides in the genome means that if an individual genome is only sequenced once, there will be a significant number of sequencing errors. Furthermore, many positions in a genome contain rare single-nucleotide polymorphisms (SNPs). Hence to distinguish between sequencing errors and true SNPs, it is necessary to increase the sequencing accuracy even further by sequencing individual genomes a large number of times. Ultra-deep sequencing The term "ultra-deep" can sometimes also refer to higher coverage (>100-fold), which allows for detection of sequence variants in mixed populations. In the extreme, error-corrected sequ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Αr15 RNA
αr15 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Rhizobiales. The first members of this family (''smr15C1'' and ''smrC15C2'') were found tandemly arranged in the same intergenic region (IGR) of the ''Sinorhizobium meliloti'' 1021 chromosome (C). Further homology and structure conservation analysis have identified full-length Smr15C1 and Smr15C2 homologs in several nitrogen-fixing symbiotic rhizobia (i.e. ''R. leguminosarum'' bv. viciae, ''R. leguminosarum'' bv. trifolii, ''R. etli'', and several ''Mesorhizobium'' species), in the plant pathogens belonging to ''Agrobacterium'' species (i.e. ''A. tumefaciens'', ''A. vitis'', ''A. radiobacter'', and ''Agrobacterium'' H13) as well as in a broad spectrum of ''Brucella'' species (''B. ovis'', ''B. canis'', ''B. abortus'' and ''B. microtis'', and several biovars of ''B. melitensis''). The Smr15C1 (115 nt) and Smr15C2 (121 nt) homologs are also encoded in tand ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Brucella Abortus
''Brucella abortus'' is a Gram-negative bacterium in the family Brucellaceae and is one of the causative agents of brucellosis. The rod-shaped pathogen is classified under the domain Bacteria. The prokaryotic ''B. abortus'' is non-spore-forming, non-motile and aerobic. Transmission ''Brucella abortus'' enters phagocytes that invade human and animal innate defenses which in turn, cause chronic disease in the host. The liver and spleen are the mainly affected areas of the body. Farm workers and veterinarians are the highest risk individuals for acquiring the disease due to their close proximity to the animals. Swine, goats, sheep, and cattle are a few of the reservoirs for the disease. ''B. abortus'' causes abortion and infertility in adult cattle and is a zoonosis which is present worldwide. Humans are commonly infected after drinking unpasteurized milk from affected animals or, less commonly, when coming into contact with infected tissues and liquids (afterbirth, etc.). The i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hfq Protein
The Hfq protein (also known as HF-I protein) encoded by the ''hfq'' gene was discovered in 1968 as an ''Escherichia coli'' host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles that are usually mediated by interacting with Hfq binding sRNA. In ''E. coli'', Hfq mutants show multiple stress response related phenotypes. The Hfq protein is now known to regulate the translation of two major stress transcription factors ( σS (RpoS) and σE (RpoE) ) in Enterobacteria. It also regulates sRNA in ''Vibrio cholerae'', a specific example being MicX sRNA. In ''Salmonella typhimurium'', Hfq has been shown to be an essential virulence factor as its deletion attenuates the ability of ''S.typhimurium'' to invade epithelial cells, secrete virulence factors or survive in cultured macrophages. In ''Salmonella'', Hfq deletion mutants are also non motile and exhibit chro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Operon
In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be ''co-transcribed'' to define an operon. Originally, operons were thought to exist solely in prokaryotes (which includes organelles like plastids that are derived from bacteria), but since the discovery of the first operons in eukaryotes in the early 1990s, more evidence has arisen to suggest they are more common than previously assumed. In general, expression of prokaryotic operons leads to the generation of polycistronic mRNAs, while eukaryotic operons lead to monocistronic mRNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacillus Subtilis BSR SRNAs
In a screen of the ''Bacillus subtilis'' genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed ''Escherichia coli'' cells harboring a plasmid with PCR-amplified IGRs of ''B. subtilis'', indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase (4–6 h), but undetectable during the stationary phase (8 h). Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a rec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Escherichia Coli SRNA
''Escherichia coli'' contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verified experimentally. 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so the number of sRNA genes in ''E. coli'' is likely to be less than 275. A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth. A screen for sRNA genes based on homology to ''Salmonella'' and ''Klebsiella'' identified 59 candidate sRNA genes. From this set of candidate genes, microar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mycobacterium Tuberculosis SRNA
''Mycobacterium tuberculosis'' contains at least nine small RNA families in its genome. The small RNA (sRNA) families were identified through RNomics – the direct analysis of RNA molecules isolated from cultures of ''Mycobacterium tuberculosis''. The sRNAs were characterised through RACE mapping and Northern blot experiments. Secondary structures of the sRNAs were predicted using Mfold. sRNAPredict2 – a bioinformatics tool – suggested 56 putative sRNAs in ''M. tuberculosis'', though these have yet to be verified experimentally. Hfq protein homologues have yet to be found in ''M. tuberculosis''; an alternative pathway – potentially involving conserved C-rich motifs – has been theorised to enable trans-acting sRNA functionality. sRNAs were shown to have important physiological roles in ''M. tuberculosis''. Overexpression of G2 sRNA, for example, prevented growth of ''M. tuberculosis'' and greatly reduced the growth of ''M. smegmatis''; ASdes sRNA is thought to be a cis-a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Xanthomonas SRNA
In molecular biology, ''Xanthomonas'' sRNA are small RNAs which have been identified in various species of the bacterium '' Xanthomonas''. Analysis of the plant pathogen '' Xanthomonas campestris pv. vesicatoria'' revealed expression of seven cis-encoded antisense RNAs (asX1-asX7) and 15 intergenic sRNAs (sX1 - sX15). Several sRNAs have also been identified in '' Xanthomonas campestris pathovar campestris''. Some of these ''X. campestris'' sRNAs are only found in ''Xanthomonas'', some are also expressed in other bacteria. Several of these sRNAs appear to contribute to virulence, including sX12, sX13 and sRNA-Xcc1. Computational analysis predicts 63 sRNAs in '' Xanthomonas oryzae pathovar oryzae'', expression of 8 of these has been experimentally confirmed. Expression of three of these is Hfq-dependent. See also * ''Bacillus subtilis'' BSR sRNAs *Bacterial small RNA Bacterial small RNAs (bsRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
