126 research outputs found
Cytoplasmic RNA decay pathways - enzymes and mechanisms
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3â to 5â and 5â to 3â mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3â-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm
Isolation and Characterization of Pseudomonas spp. Strains That Efficiently Decompose Sodium Dodecyl Sulfate
Due to their particular properties, detergents are widely used in household cleaning products, cosmetics, pharmaceuticals, and in agriculture as adjuvants tailoring the features of pesticides or other crop protection agents. The continuously growing use of these various products means that water soluble detergents have become one of the most problematic groups of pollutants for the aquatic and terrestrial environments. Thus it is important to identify bacteria having the ability to survive in the presence of large quantities of detergent and efficiently decompose it to non-surface active compounds. In this study, we used peaty soil sampled from a surface flow constructed wetland in a wastewater treatment plant to isolate bacteria that degrade sodium dodecyl sulfate (SDS). We identified and initially characterized 36 Pseudomonas spp. strains that varied significantly in their ability to use SDS as their sole carbon source. Five isolates having the closest taxonomic relationship to the Pseudomonas jessenii subgroup appeared to be the most efficient SDS degraders, decomposing from 80 to 100% of the SDS present in an initial concentration 1 g/L in less than 24 h. These isolates exhibited significant differences in degree of SDS degradation, their resistance to high detergent concentration (ranging from 2.5 g/L up to 10 g/L or higher), and in chemotaxis toward SDS on a plate test. Mass spectrometry revealed several SDS degradation products, 1-dodecanol being dominant; however, traces of dodecanal, 2-dodecanol, and 3-dodecanol were also observed, but no dodecanoic acid. Native polyacrylamide gel electrophoresis zymography revealed that all of the selected isolates possessed alkylsulfatase-like activity. Three isolates, AP3_10, AP3_20, and AP3_22, showed a single band on native PAGE zymography, that could be the result of alkylsulfatase activity, whereas for isolates AP3_16 and AP3_19 two bands were observed. Moreover, the AP3_22 strain exhibited a band in presence of both glucose and SDS, whereas in other isolates, the band was visible solely in presence of detergent in the culture medium. This suggests that these microorganisms isolated from peaty soil exhibit exceptional capabilities to survive in, and break down SDS, and they should be considered as a valuable source of biotechnological tools for future bioremediation and industrial applications
Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150
We present the draft genome sequence of Pseudomonas jessenii type strain DSM 17150. The assembly consists of 13 contigs, contains 6,537,206 bp, and has a GC content of 59.7%
Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611
Here, we report the draft genome sequence of Pseudomonas umsongensis type strain DSM 16611. The assembly consists of 14 contigs containing 6,701,403 bp with a GC content of 59.73%
Draft Genome Sequence of the Type Strain Sphingopyxis bauzanensis DSM 22271
We present here the draft genome sequence of Sphingopyxis bauzanensis DSM 22271. The assembly contains 4,258,005 bp in 28 scaffolds and has a GC content of 63.3%. A series of specific genes involved in the catabolism or transport of aromatic compounds was identified
Pseudomonas silesiensis sp. nov. strain A3 T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence
Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp. has been described as a microorganism that can easily adapt to new environmental conditions due to its resistance to the presence of high concentrations of heavy metals or chemical pollution. Here we present the isolation and analysis of Pseudomonas silesiensis sp. nov. strain A3T isolated from peaty soil used in a biological wastewater treatment plant exploited by a pesticide packaging company. Phylogenetic MLSA analysis of 4 housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), complete genome sequence comparison (ANIb, Tetranucleotide identity, digital DDH), FAME analysis, and other biochemical tests indicate the A3T strain (type strain PCM 2856T=DSM 103370T) differs significantly from the closest relative species and therefore represents a new species within the Pseudomonas genus. Moreover, bioinformatic analysis of the complete sequenced genome showed that it consists of 6,823,539bp with a 59.58mol% G+C content and does not contain any additional plasmids. Genome annotation predicted the presence of 6066 genes, of which 5875 are coding proteins and 96 are RNA genes
Draft Genome Sequence of the Type Strain Sphingopyxis witflariensis DSM 14551
Here, we present the draft genome sequence of Sphingopyxis witflariensis strain DSM 14551. The assembly consists of 38 contigs and contains 4,306,761 bp, with a GC content of 63.3%
Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs
The exosome-independent exoribonuclease DIS3L2
is mutated in Perlman syndrome. Here, we used extensive
global transcriptomic and targeted biochemical
analyses to identify novel DIS3L2 substrates in
human cells. We show that DIS3L2 regulates pol
II transcripts, comprising selected canonical and
histone-coding mRNAs, and a novel FTL short RNA
from the ferritin mRNA 5ïżœ UTR. Importantly, DIS3L2
contributes to surveillance of maturing snRNAs during
their cytoplasmic processing. Among pol III transcripts,
DIS3L2 particularly targets vault and Y RNAs
and an Alu-like element BC200 RNA, but not Alu repeats,
which are removed by exosome-associated
DIS3. Using 3ïżœ RACE-Seq, we demonstrate that
all novel DIS3L2 substrates are uridylated in vivo
by TUT4/TUT7 poly(U) polymerases. Uridylationdependent
DIS3L2-mediated decay can be recapitulated
in vitro, thus reinforcing the tight cooperation
between DIS3L2 and TUTases. Together these results
indicate that catalytically inactive DIS3L2, characteristic
of Perlman syndrome, can lead to deregulation
of its target RNAs to disturb transcriptome homeostasis
A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans.
The exosome complex is a major eukaryotic exoribonuclease that requires the SKI complex for its activity in the cytoplasm. In yeast, the Ski7 protein links both complexes, whereas a functional equivalent of the Ski7 has remained unknown in the human genome.Proteomic analysis revealed that a previously uncharacterized short splicing isoform of HBS1L (HBS1LV3) is the long-sought factor linking the exosome and SKI complexes in humans. In contrast, the canonical HBS1L variant, HBS1LV1, which acts as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. Interestingly, both HBS1LV1 and HBS1LV3 interact with the SKI complex and HBS1LV1 seems to antagonize SKI/exosome supercomplex formation. HBS1LV3 contains a unique C-terminal region of unknown structure, with a conserved RxxxFxxxL motif responsible for exosome binding and may interact with the exosome core subunit RRP43 in a way that resembles the association between Rrp6 RNase and Rrp43 in yeast. HBS1LV3 or the SKI complex helicase (SKI2W) depletion similarly affected the transcriptome, deregulating multiple genes. Furthermore, half-lives of representative upregulated mRNAs were increased, supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway, essential for transcriptome homeostasis in the cytoplasm
Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria
Maintenance of mitochondrial gene expression is
crucial for cellular homeostasis. Stress conditions
may lead to a temporary reduction of mitochondrial
genome copy number, raising the risk of insufficient
expression of mitochondrial encoded genes. Little
is known how compensatory mechanisms operate
to maintain proper mitochondrial transcripts levels
upon disturbed transcription and which proteins are
involved in them. Here we performed a quantitative
proteomic screen to search for proteins that sustain
expression of mtDNA under stress conditions. Analysis
of stress-induced changes of the human mitochondrial
proteome led to the identification of several
proteins with poorly defined functions among which
we focused on C6orf203, which we named MTRES1
(Mitochondrial Transcription Rescue Factor 1). We
found that the level of MTRES1 is elevated in cells
under stress and we show that this upregulation of
MTRES1 prevents mitochondrial transcript loss under
perturbed mitochondrial gene expression. This
protective effect depends on the RNA binding activity
of MTRES1. Functional analysis revealed that
MTRES1 associates with mitochondrial RNA polymerase
POLRMT and acts by increasing mitochondrial
transcription, without changing the stability of
mitochondrial RNAs. We propose that MTRES1 is an
example of a protein that protects the cell from mitochondrial
RNA loss during stress
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