1461 research outputs found
Sort by
Three-layered control of mRNA poly(A) tail synthesis in Saccharomyces cerevisiae
No full textBiogenesis of most eukaryotic mRNAs involves the addition of an untemplated polyadenosine (pA) tail by the cleavage and polyadenylation machinery. The pA tail, and its exact length, impacts mRNA stability, nuclear export, and translation. To define how polyadenylation is controlled in S. cerevisiae, we have used an in vivo assay capable of assessing nuclear pA tail synthesis, analyzed tail length distributions by direct RNA sequencing, and reconstituted polyadenylation reactions with purified components. This revealed three control mechanisms for pA tail length. First, we found that the pA binding protein (PABP) Nab2p is the primary regulator of pA tail length. Second, when Nab2p is limiting, the nuclear pool of Pab1p, the second major PABP in yeast, controls the process. Third, when both PABPs are absent, the cleavage and polyadenylation factor (CPF) limits pA tail synthesis. Thus, Pab1p and CPF provide fail-safe mechanisms to a primary Nab2p-dependent pathway, thereby preventing uncontrolled polyadenylation and allowing mRNA export and translation
Unexplored potential: Biologically active compounds produced by microorganisms from hard-to-reach environments and their applications
Get PDFRapid development of antibiotic resistance of bacteria
and fungi, as well as cancer drug resistance, has become
a global medical problem. Therefore, alternative
methods of treatment are considered. Studies of recent
years have focused on finding new biologically active
compounds that may be effective against drug-resistant
cells. High biodiversity of hard-to-reach environments
offers sources to search for novel molecules potentially
applicable for medical purposes. In this review article,
we summarize and discuss compounds produced by
microorganisms from hot springs, glaciers, caves, underground lakes, marine ecosystems, and hydrothermal
vents. Antibacterial, antiviral, antifungal, anticancer, antiinflammatory,
and antioxidant potential of these molecules
are presented and discussed. We conclude that using
compounds derived from microorganisms occurring
in extreme environments might be considered in further
studies on development of treatment procedures for diseases
caused by drug-resistant cells
Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Get PDFpCTX-M3—Structure, Function, and Evolution of a Multi-Resistance Conjugative Plasmid of a Broad Recipient Range
Get PDFpCTX-M3 is the archetypic member of the IncM incompatibility group of conjugative
plasmids (recently referred to as IncM2). It is responsible for the worldwide dissemination of
numerous antibiotic resistance genes, including those coding for extended-spectrum β-lactamases
and conferring resistance to aminoglycosides. The IncM plasmids acquired during evolution diverse
mobile genetic elements found in one or two multiple resistance regions, MRR(s), grouping antibiotic
resistance genes as well as mobile genetic elements or their remnants. The IncM plasmids can be
found in bacteria inhabiting various environments. The information on the structure and biology of
pCTX-M3 is integrated in this review. It focuses on the functional modules of pCTX-M3 responsible
for its replication, stable maintenance, and conjugative transfer, indicating that the host range of the
pCTX-M3 replicon is limited to representatives of the family Enterobacteriaceae (Enterobacterales
ord. nov.), while the range of recipients of its conjugation system is wide, comprising Alpha-, Beta-,
and Gammaproteobacteria, and also Firmicutes
Dynamics and Complexity of Dark Fermentation Microbial Communities Producing Hydrogen From Sugar Beet Molasses in Continuously Operating Packed Bed Reactors
Get PDFThis study describes the dynamics and complexity of microbial communities producing hydrogen-rich fermentation gas from sugar-beet molasses in five packed-bed reactors (PBRs). The bioreactors constitute a part of a system producing hydrogen from the by-products of the sugar-beet industry that has been operating continuously in one of the Polish sugar factories. PBRs with different working volumes, packing materials, construction and inocula were tested. This study focused on analysis (based on 16S rRNA profiling and shotgun metagenomics sequencing) of the microbial communities selected in the PBRs under the conditions of high (>100 cm3/g COD of molasses) and low (<50 cm3/g COD of molasses) efficiencies of hydrogen production. The stability and efficiency of the hydrogen production are determined by the composition of dark fermentation microbial communities. The most striking difference between the tested samples is the ratio of hydrogen producers to lactic acid bacteria. The highest efficiency of hydrogen production (130–160 cm3/g COD of molasses) was achieved at the ratios of HPB to LAB ≈ 4:2.5 or 2.5:1 as determined by 16S rRNA sequencing or shotgun metagenomics sequencing, respectively. The most abundant Clostridium species were C. pasteurianum and C. tyrobutyricum. A multiple predominance of LAB over HPB (3:1–4:1) or clostridia over LAB (5:1–60:1) results in decreased hydrogen production. Inhibition of hydrogen production was illustrated by overproduction of short chain fatty acids and ethanol. Furthermore, concentration of ethanol might be a relevant marker or factor promoting a metabolic shift in the DF bioreactors processing carbohydrates from hydrogen-yielding toward lactic acid fermentation or solventogenic pathways. The novelty of this study is identifying a community balance between hydrogen producers and lactic acid bacteria for stable hydrogen producing systems. The balance stems from long-term selection of hydrogen-producing microbial community, operating conditions such as bioreactor construction, packing material, hydraulic retention time and substrate concentration. This finding is confirmed by additional analysis of the proportions between HPB and LAB in dark fermentation bioreactors from other studies. The results contribute to the advance of knowledge in the area of relationships and nutritional interactions especially the cross-feeding of lactate between bacteria in dark fermentation microbial communities
Coastal regions of the northern Antarctic Peninsula are key for gentoo populations
Get PDFSouthern Ocean ecosystems are rapidly changing due to climate variability. An apparent beneficiary of such change in the western Antarctic Peninsula (WAP) is the gentoo penguin Pygoscelis papua, which has increased its population size and expanded its range southward in the last 20 years. To better understand how this species has responded to large-scale changes, we tracked individuals during the non-breeding winter period from five colonies across the latitudinal range of breeding sites in the WAP, including from a recently established colony. Results highlight latitudinal gradients in movement; strong associations with shallow, coastal habitats along the entire Antarctic Peninsula; and movements that are independent of, yet constrained by, sea ice. It is clear that coastal habitats essential to gentoo penguins during the breeding season are similarly critical during winter. Larger movements of birds from northern colonies in the WAP further suggest that leap-frog migration may influence colonization events by facilitating nest-area prospecting and use of new haul-out sites. Our results support efforts to develop a marine protected area around the WAP. Winter habitats used by gentoo penguins outline high priority areas for improving the management of the spatiotemporally concentrated krill (Euphausia superba) fishery that operates in this region during winter
The Adaptive Landscape of Genetic Interaction Network Has No Impact on Yeast Adaptive Evolution
No full textSpecific Features of RNA Polymerases I and III: Structure and Assembly
Get PDFRNA polymerase I (RNAPI) and RNAPIII are multi-heterogenic protein complexes that specialize in the transcription of highly abundant non-coding RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA). In terms of subunit number and structure, RNAPI and RNAPIII are more complex than RNAPII that synthesizes thousands of different mRNAs. Specific subunits of the yeast RNAPI and RNAPIII form associated subcomplexes that are related to parts of the RNAPII initiation factors. Prior to their delivery to the nucleus where they function, RNAP complexes are assembled at least partially in the cytoplasm. Yeast RNAPI and RNAPIII share heterodimer Rpc40-Rpc19, a functional equivalent to the αα homodimer which initiates assembly of prokaryotic RNAP. In the process of yeast RNAPI and RNAPIII biogenesis, Rpc40 and Rpc19 form the assembly platform together with two small, bona fide eukaryotic subunits, Rpb10 and Rpb12. We propose that this assembly platform is co-translationally seeded while the Rpb10 subunit is synthesized by cytoplasmic ribosome machinery. The translation of Rpb10 is stimulated by Rbs1 protein, which binds to the 3′-untranslated region of RPB10 mRNA and hypothetically brings together Rpc19 and Rpc40 subunits to form the αα-like heterodimer. We suggest that such a co-translational mechanism is involved in the assembly of RNAPI and RNAPIII complexes
Proteomic analysis of pikeperch seminal plasma provides novel insight into the testicular development of domesticated fish stocks
Get PDFControl of the reproduction of domesticated stocks is considered a prerequisite for aquaculture development of pikeperch. However, knowledge about the physiology of
the captive pikeperch male reproductive system and the biology of semen is very limited, especially regarding protein characteristics. The aims of our study were to
characterize pikeperch sperm quantity and quality parameters and to analyze changes in the proteome of the same males spawned for the first and second times. Moreover,
attempts were made to generate the first proteomic library of seminal plasma proteins. Semen collected during the first spawning season were was characterized by lower
sperm concentration and volume than for the second season. Using mass spectrometry-based label-free quantitative proteomics, we identified 850 proteins in the
seminal plasma of pikeperch from both spawning seasons, and 65 seminal proteins were found to be differentially abundant between the first and second spawning seasons. The majority of differentially abundant proteins were involved in stress and immune responses, developmental processes, cofactor metabolic processes, proteolysis, cellular oxidant detoxification and organization of the extracellular matrix
(ECM). In addition, several proteins unique to pikeperch seminal plasma were identified, including antifreeze proteins, hibernation-specific plasma proteins, lectins
and vitellogenin. In summary, our results indicate that males that spawned for the first time were characterized by incompletely mature gonads and the expression of proteins
associated with the early phase of spermatogenesis and ECM organization. On the other hand, males that spawned for the second time exhibited advanced gonadal maturation and expression of proteins related to the late stage of spermatogenesis and sperm maturation, including regulation of reactive oxygen species generation, bicarbonate production, sperm elongation and separation. The identification of a large number of seminal plasma proteins provides a valuable resource for understanding the
functions of seminal plasma and the molecular mechanisms involved in testicular development and maturation in domesticated fish, which is a prerequisite for better
control of reproduction in captivity
Succinate Dehydrogenase-Deficient Renal Cancer Featuring Fructose-1,6-Biphosphatase Loss, Pyruvate Kinase M2 Overexpression, and SWI/SNF Chromatin Remodeling Complex Aberrations: A Rare Case Report
Get PDFSuccinate dehydrogenase (SDH)-deficient renal cancer is
a rare renal cancer subtype recently accepted by the
World Health Organization as a unique subtype of renal
cell carcinoma (RCC). Here we report a case of 17-year old man. The detailed evaluation indicated occurrence
of the SDHB-deficient RCC. The genetic testing revealed
no germline mutation in SDH genes. Immunohistochemistry showed SDHB deficiency, overexpression of pyruvate kinase M2 and dramatic downregulation of
fructose-1,6-bisphosphatase metabolic enzymes, and
unaltered levels of phosphorylated AMP-activated
protein kinase and mammalian target of rapamycin.
Strong upregulation of INI1 and BRG1 and overexpression of BAF180, subunits of SWI/SNF ATP-dependent chromatin remodeling complex, were also
found. The identified tumor pathologically did not
resemble clear cell renal cell carcinoma (ccRCC), but
some metabolic alterations are common for both cancer
types. Thus, we postulate that the phenotypical differences between ccRCC and SDHB-deficient RCC may be
related to distinct molecular and metabolic alterations