-
International Journal of Molecular... Aug 2022Among proteins that interact with DNA or RNA, more or less specifically, there is a special group of relatively small polypeptides which are present in prokaryotic cells...
Among proteins that interact with DNA or RNA, more or less specifically, there is a special group of relatively small polypeptides which are present in prokaryotic cells and interact with nucleic acids [...].
Topics: DNA; Nucleic Acids; Prokaryotic Cells; RNA
PubMed: 36077274
DOI: 10.3390/ijms23179876 -
Microbiome May 2017Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of...
BACKGROUND
Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts. Anaerobic digesters are ideal model systems to examine phage-host interaction, owing to easy access, stable operation, nutrient-rich environment, and consequently enormous numbers of phages and prokaryotic cells.
RESULTS
Equipped with high-throughput, cutting-edge environmental genomics techniques, we examined phage and prokaryotic community composition of four anaerobic digesters in full-scale wastewater treatment plants across China. Despite the relatively stable process performance in biogas production, phage and prokaryotic groups fluctuated monthly over a year of study period, showing significant correlations between those two groups at the α- and β-diversity levels. Strikingly, phages explained 40.6% of total variations of the prokaryotic community composition, much higher than the explanatory power by abiotic factors (14.5%). Consequently, phages were significantly (P < 0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed phage-prokaryote pairs were shallowly conserved since they were detected only within small viral clades.
CONCLUSIONS
Those results collectively demonstrate phages as a major biotic factor in controlling prokaryotic composition and process performance. Therefore, phages may play a larger role in shaping prokaryotic community dynamics and process performance of anaerobic digesters than currently appreciated.
Topics: Anaerobiosis; Bacteriophages; Biofuels; Phylogeny; Prokaryotic Cells; Seasons; Sequence Analysis, DNA; Wastewater; Water Purification
PubMed: 28569210
DOI: 10.1186/s40168-017-0272-8 -
Biochemistry. Biokhimiia Jan 2023In 1994 a new class of prokaryotic compartments was discovered, collectively called "encapsulins" or "nanocompartments". Encapsulin shell protomer proteins self-assemble... (Review)
Review
In 1994 a new class of prokaryotic compartments was discovered, collectively called "encapsulins" or "nanocompartments". Encapsulin shell protomer proteins self-assemble to form icosahedral structures of various diameters (24-42 nm). Inside of nanocompartments shells, one or several cargo proteins, diverse in their functions, can be encapsulated. In addition, non-native cargo proteins can be loaded into nanocompartments, and shell surfaces can be modified via various compounds, which makes it possible to create targeted drug delivery systems, labels for optical and MRI imaging, and to use encapsulins as bioreactors. This review describes a number of strategies of encapsulins application in various fields of science, including biomedicine and nanobiotechnologies.
Topics: Bacterial Proteins; Biotechnology; Prokaryotic Cells; Protein Subunits; Drug Delivery Systems
PubMed: 37068871
DOI: 10.1134/S0006297923010042 -
Current Biology : CB May 2021All living cells depend on the intricate organization of molecular components in space and time. Although this notion was historically based on eukaryotic cells, with...
All living cells depend on the intricate organization of molecular components in space and time. Although this notion was historically based on eukaryotic cells, with their structured intracellular architecture and cellular morphologies, it is now recognized that prokaryotes (that is, bacteria and archaea) also possess complex structures. A cytoskeleton is a network of intracellular protein filaments that play a structural or mechanical role (such as scaffolding, pushing, or pulling) in the spatiotemporal organization of cellular processes. Polymerization of protein monomers in a roughly linear fashion into filaments represents an effective means to establish long-range spatial order by bridging the gap between nanometer-sized molecules and micron-sized cells. It is now evident that bacteria and archaea possess numerous kinds of cytoskeletal proteins, including prokaryotic homologues of the eukaryotic actins, tubulins, and intermediate filaments, as well as other types that have been found primarily or exclusively in prokaryotes (Table 1). Understanding the diverse functions and mechanisms of the rapidly growing universe of prokaryotic cytoskeletal proteins will not only advance prokaryotic cell biology and reveal evolutionary principles, but also open up new avenues for the development of anti-microbial agents, de novo protein design, and the construction of minimal and synthetic cells.
Topics: Archaea; Bacteria; Cytoskeletal Proteins; Cytoskeleton; Prokaryotic Cells
PubMed: 34033787
DOI: 10.1016/j.cub.2021.03.011 -
Proceedings of the National Academy of... Aug 2015Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular... (Review)
Review
Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote "discontinuity." Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.
Topics: Animals; Biological Evolution; Energy Metabolism; Escherichia coli; Eukaryota; Eukaryotic Cells; Evolution, Molecular; Genome, Bacterial; Humans; Introns; Mitochondria; Origin of Life; Phenotype; Phylogeny; Plants; Prokaryotic Cells; Spliceosomes
PubMed: 25883267
DOI: 10.1073/pnas.1421376112 -
Philosophical Transactions of the Royal... Nov 2018Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of... (Review)
Review
Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
Topics: Bacteria; Poly A; Polyadenylation; Prokaryotic Cells; RNA
PubMed: 30397102
DOI: 10.1098/rstb.2018.0166 -
Cellular and Molecular Life Sciences :... Jul 2016Glucan-branching enzyme plays an essential role in the formation of branched polysaccharides, glycogen, and amylopectin. Only one type of branching enzyme, belonging to... (Review)
Review
Glucan-branching enzyme plays an essential role in the formation of branched polysaccharides, glycogen, and amylopectin. Only one type of branching enzyme, belonging to glycoside hydrolase family 13 (GH13), is found in eukaryotes, while two types of branching enzymes (GH13 and GH57) occur in prokaryotes (Bacteria and Archaea). Both of these types are the members of protein families containing the diverse specificities of amylolytic glycoside hydrolases. Although similarities are found in the catalytic mechanism between the two types of branching enzyme, they are highly distinct from each other in terms of amino acid sequence and tertiary structure. Branching enzymes are found in 29 out of 30 bacterial phyla and 1 out of 5 archaeal phyla, often along with glycogen synthase, suggesting the existence of α-glucan production and storage in a wide range of prokaryotes. Enormous variability is observed as to which type and how many copies of branching enzyme are present depending on the phylum and, in some cases, even among species of the same genus. Such a variation may have occurred through lateral transfer, duplication, and/or differential loss of genes coding for branching enzyme during the evolution of prokaryotes.
Topics: Biocatalysis; Glucans; Glycoside Hydrolases; Phylogeny; Prokaryotic Cells; Substrate Specificity
PubMed: 27141939
DOI: 10.1007/s00018-016-2243-9 -
IUBMB Life Apr 2015Persulfide groups are chemically versatile and participate in a wide array of biochemical pathways. Although it is well documented that persulfurated proteins supply a... (Review)
Review
Persulfide groups are chemically versatile and participate in a wide array of biochemical pathways. Although it is well documented that persulfurated proteins supply a number of important and elaborate biosynthetic pathways with sulfane sulfur, it is far less acknowledged that the enzymatic generation of persulfidic sulfur, the successive transfer of sulfur as a persulfide between multiple proteins, and the oxidation of sulfane sulfur in protein-bound form are also essential steps during dissimilatory sulfur oxidation in bacteria and archaea. Here, the currently available information on sulfur trafficking in sulfur oxidizing prokaryotes is reviewed, and the idea is discussed that sulfur is always presented to cytoplasmic oxidizing enzymes in a protein-bound form, thus preventing the occurrence of free sulfide inside of the prokaryotic cell. Thus, sulfur trafficking emerges as a central element in sulfur-oxidizing pathways, and TusA homologous proteins appear to be central and common elements in these processes.
Topics: Cytoplasm; Oxidation-Reduction; Prokaryotic Cells; Sulfur
PubMed: 25913822
DOI: 10.1002/iub.1371 -
International Journal of Molecular... Apr 2022Stress is an inevitable part of life. An organism is exposed to multiple stresses and overcomes their negative consequences throughout its entire existence. A... (Review)
Review
Stress is an inevitable part of life. An organism is exposed to multiple stresses and overcomes their negative consequences throughout its entire existence. A correlation was established between life expectancy and resistance to stress, suggesting a relationship between aging and the ability to respond to external adverse effects as well as quickly restore the normal regulation of biological processes. To combat stress, cells developed multiple pro-survival mechanisms, one of them is the assembly of special stress-induced membraneless organelles (MLOs). MLOs are formations that do not possess a lipid membrane but rather form as a result of the "liquid-liquid" phase separation (LLPS) of biopolymers. Stress-responsive MLOs were found in eukaryotes and prokaryotes, they form as a reaction to the acute environmental conditions and are dismantled after its termination. These compartments function to prevent damage to the genetic and protein material of the cell during stress. In this review, we discuss the characteristics of stress-induced MLO-like structures in eukaryotic and prokaryotic cells.
Topics: Biomolecular Condensates; Eukaryota; Organelles; Prokaryotic Cells; Proteins
PubMed: 35563401
DOI: 10.3390/ijms23095010 -
Nature Jun 2023In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the...
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
Topics: Archaea; Eukaryota; Eukaryotic Cells; Phylogeny; Prokaryotic Cells; Datasets as Topic; Gene Duplication; Evolution, Molecular
PubMed: 37316666
DOI: 10.1038/s41586-023-06186-2