Comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source ...of the mitochondrial genome in contemporary eukaryotes. A surprising result of phylogenetic analyses is the relatively small proportion (10–20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. A large fraction of mitochondrial proteins typically has detectable homologs only in other eukaryotes and is presumed to represent proteins that emerged specifically within eukaryotes. A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.
Mitochondrial evolution Gray, Michael W
Cold Spring Harbor perspectives in biology,
2012-Sep-01, 2012-09-01, 20120901, Letnik:
4, Številka:
9
Journal Article
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Viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria). ...Accordingly, the endosymbiont hypothesis--the idea that the mitochondrion evolved from a bacterial progenitor via symbiosis within an essentially eukaryotic host cell--has assumed the status of a theory. Yet mitochondrial genome evolution has taken radically different pathways in diverse eukaryotic lineages, and the organelle itself is increasingly viewed as a genetic and functional mosaic, with the bulk of the mitochondrial proteome having an evolutionary origin outside Alphaproteobacteria. New data continue to reshape our views regarding mitochondrial evolution, particularly raising the question of whether the mitochondrion originated after the eukaryotic cell arose, as assumed in the classical endosymbiont hypothesis, or whether this organelle had its beginning at the same time as the cell containing it.
The 1967 article "On the Origin of Mitosing Cells" in the
by Lynn Margulis (then Lynn Sagan) is widely regarded as stimulating renewed interest in the long-dormant endosymbiont hypothesis of ...organelle origins. In her article, not only did Margulis champion an endosymbiotic origin of mitochondria and plastids from bacterial ancestors, but she also posited that the eukaryotic flagellum (undulipodium in her usage) and mitotic apparatus originated from an endosymbiotic, spirochete-like organism. In essence, she presented a comprehensive symbiotic view of eukaryotic cell evolution (eukaryogenesis). Not all of the ideas in her article have been accepted, for want of compelling evidence, but her vigorous promotion of the role of symbiosis in cell evolution unquestionably had a major influence on how subsequent investigators have viewed the origin and evolution of mitochondria and plastids and the eukaryotic cell per se.
The term “RNA editing” encompasses a wide variety of mechanistically and phylogenetically unrelated processes that change the nucleotide sequence of an RNA species relative to that of the encoding ...DNA. Two general classes of editing, substitution and insertion/deletion, have been described, with all major types of cellular RNA (messenger, ribosomal, and transfer) undergoing editing in different organisms. In cases where RNA editing is required for function (e.g., to generate a translatable open reading frame in a mRNA), editing is an obligatory step in the pathway of genetic information expression. How, when, and why individual RNA editing systems originated are intriguing biochemical and evolutionary questions. Here I review briefly what is known about the biochemistry, genetics, and phylogenetics of several very different RNA editing systems, emphasizing what we can deduce about their origin and evolution from the molecular machinery involved. An evolutionary model, centered on the concept of “constructive neutral evolution”, is able to account in a general way for the origin of RNA editing systems. The model posits that the biochemical elements of an RNA editing system must be in place before there is an actual need for editing, and that RNA editing systems are inherently mutagenic because they allow potentially deleterious or lethal mutations to persist at the genome level, whereas they would otherwise be purged by purifying selection.
Piece by piece: Building a ribozyme Gray, Michael W.; Gopalan, Venkat
The Journal of biological chemistry,
02/2020, Letnik:
295, Številka:
8
Journal Article
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The ribosome and RNase P are cellular ribonucleoprotein complexes that perform peptide bond synthesis and phosphodiester bond cleavage, respectively. Both are ancient biological assemblies that were ...already present in the last universal common ancestor of all life. The large subunit rRNA in the ribosome and the RNA subunit of RNase P are the ribozyme components required for catalysis. Here, we explore the idea that these two large ribozymes may have begun their evolutionary odyssey as an assemblage of RNA “fragments” smaller than the contemporary full-length versions and that they transitioned through distinct stages along a pathway that may also be relevant for the evolution of other non-coding RNAs.
Injection drug use (IDU) is a growing public health threat in Virginia, though there is limited knowledge of related morbidity. The purpose of this study was to describe the temporal, geographic and ...clinical trends and characteristics of infective endocarditis associated with IDU (IDU-IE) and to identify opportunities for better-quality care of people who inject drugs (PWID).
We reviewed charts for all admissions coded for both IE and drug use disorders at the University of Virginia Medical Center (UVA) from January 2000 to July 2016. A random sample of 30 admissions coded for IE per year were reviewed to evaluate temporal trends in the proportion of IDU associated IE cases.
There were a total of 76 patients with IDU-IE during the study period, 7.54-fold increase (prevalence ratio: 8.54, 95% CI 3.70-19.72) from 2000 to 2016. The proportion of IE that was IDU-associated increased by nearly 10% each year (prevalence ratio of IDU per year: 1.09, 95% CI: 1.05-1.14). Patients with IDU-IE had longer hospital stays median days (interquartile range); IDU-IE, 17 (10-29); non-IDU-IE, 10 (6-18); p-value = 0.001 with almost twice the cost of admission as those without IDU median (interquartile range); IDU-IE, $47,899 ($24,578-78,144); non-IDU-IE, $26,460 ($10,220-60,059); p-value = 0.001. In 52% of cases there was no documentation of any discussion regarding addiction treatment.
IDU-IE is a severe infection that leads to significant morbidity and healthcare related costs. IDU-IE rates are increasing and will likely continue to do so without targeted interventions to help PWID. The diagnosis and treatment of IDU-IE provides an opportunity for the delivery of addiction treatment, counseling, and harm reduction strategies.
Molecular networks governing responses to targeted therapies in cancer cells are complex dynamic systems that demonstrate nonintuitive behaviors. We applied a novel computational strategy to infer ...probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell-cycle arrest caused by inhibition of MEK1/2. Through simulation of a reverse-engineered Bayesian network model, we generated predictions of G
-S transition. The model identified known components of the cell-cycle machinery, such as CCND1, CCNE2, and CDC25A, as well as revealed novel regulators of G
-S transition, IER2, TRIB1, TRIM27. Experimental validation of model predictions confirmed 10 of 12 predicted genes to have a role in G
-S progression. Further analysis showed that TRIB1 regulated the cyclin D1 promoter via NFκB and AP-1 sites and sensitized cells to TRAIL-induced apoptosis. In clinical specimens of breast cancer, TRIB1 levels correlated with expression of NFκB and its target genes (
), and TRIB1 copy number and expression were predictive of clinical outcome. Together, our results establish a critical role of TRIB1 in cell cycle and survival that is mediated via the modulation of NFκB signaling.
.
5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs ...(rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.
Abstract Background Veliparib is a potent small molecule inhibitor of PARP-1/2, which is cytotoxic in tumor cells with deficiencies in BRCA1 or BRCA2 . We studied the clinical activity and toxicity ...of veliparib in ovarian cancer patients carrying a germline BRCA1 or BRCA2 mutation ( gBRCA ). Methods Eligibility included three or fewer prior chemotherapy regimens, measurable disease and no prior use of a PARP inhibitor. Veliparib was administered at 400 mg orally BID with one cycle being 28 days. The two-stage Simon design was capable of detecting a 25% response probability with 90% power while controlling alpha = 10% (at a 10% assumed null response probability). Results The median age of the 50 eligible patients was 57 years (range 37–94) and 14, 18, and 18 patients had 1, 2, and 3 prior therapies respectively. Thirty patients (60%) were platinum-resistant. The median number of cycles administered was 6 (1–27). There was one grade 4 thrombocytopenia. Grade 3 adverse events were: fatigue (n = 3), nausea (2), leukopenia (1), neutropenia (1), dehydration (1), and ALT (1). Grade 2 events > 10% were: nausea (46%), fatigue (26%), vomiting (18%), and anemia (14%). The proportion responding was 26% (90% CI: 16%–38%, CR: 2, PR: 11); for platinum-resistant and platinum-sensitive patients the proportion responding was 20% and 35%, respectively. The most common reason for treatment discontinuation was progression (62%). Twenty-nine patients are alive; two with SD remain on veliparib. The median PFS is 8.18 months. Conclusions The single agent efficacy and tolerability of veliparib for BRCA mutation-associated recurrent ovarian cancer warrants further investigation.
The most bacteria-like mitochondrial genome known is that of the jakobid flagellate Reclinomonas americana NZ. This genome also encodes the largest known gene set among mitochondrial DNAs (mtDNAs), ...including the RNA subunit of RNase P (transfer RNA processing), a reduced form of transfer-messenger RNA (translational control), and a four-subunit bacteria-like RNA polymerase, which in other eukaryotes is substituted by a nucleus-encoded, single-subunit, phage-like enzyme. Further, protein-coding genes are preceded by potential Shine-Dalgarno translation initiation motifs. Whether similarly ancestral mitochondrial characters also exist in relatives of R. americana NZ is unknown. Here, we report a comparative analysis of nine mtDNAs from five distant jakobid genera: Andalucia, Histiona, Jakoba, Reclinomonas, and Seculamonas. We find that Andalucia godoyi has an even larger mtDNA gene complement than R. americana NZ. The extra genes are rpl35 (a large subunit mitoribosomal protein) and cox15 (involved in cytochrome oxidase assembly), which are nucleus encoded throughout other eukaryotes. Andalucia cox15 is strikingly similar to its homolog in the free-living α-proteobacterium Tistrella mobilis. Similarly, a long, highly conserved gene cluster in jakobid mtDNAs, which is a clear vestige of prokaryotic operons, displays a gene order more closely resembling that in free-living α-proteobacteria than in Rickettsiales species. Although jakobid mtDNAs, overall, are characterized by bacteria-like features, they also display a few remarkably divergent characters, such as 3'-tRNA editing in Seculamonas ecuadoriensis and genome linearization in Jakoba libera. Phylogenetic analysis with mtDNA-encoded proteins strongly supports monophyly of jakobids with Andalucia as the deepest divergence. However, it remains unclear which α-proteobacterial group is the closest mitochondrial relative.
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