scholarly journals Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA

2012 ◽  
Vol 30 (2) ◽  
pp. 310-314 ◽  
Author(s):  
Felipe S. Barreto ◽  
Ronald S. Burton

Abstract Rapid evolution of mitochondrial DNA (mtDNA) places intrinsic selective pressures on many nuclear genes involved in mitochondrial functions. Mitochondrial ribosomes, for example, are composed of mtDNA-encoded ribosomal RNAs (rRNAs) and a set of more than 60 nuclear-encoded ribosomal proteins (mRP) distinct from the cytosolic RPs (cRP). We hypothesized that the rapid divergence of mt-rRNA would result in rapid evolution of mRPs relative to cRPs, which respond to slowly evolving nuclear-encoded rRNA. In comparisons of rates of nonsynonymous and synonymous substitutions between a pair of divergent populations of the copepod Tigriopus californicus, we found that mRPs showed elevated levels of amino acid changes relative to cRPs. This pattern was equally strong at the interspecific level, between three pairs of sister species (Nasonia vitripennis vs. N. longicornis, Drosophila melanogaster vs. D. simulans, and Saccharomyces cerevisae vs. S. paradoxus). This high rate of mRP evolution may result in intergenomic incompatibilities between taxonomic lineages, and such incompatibilities could lead to dysfunction of mitochondrial ribosomes and the loss of fitness observed among interpopulation hybrids in T. californicus and interspecific hybrids in other species.

1980 ◽  
Vol 43 (1) ◽  
pp. 119-136
Author(s):  
H. Smith-Johannsen ◽  
D. Fromson ◽  
S.P. Gibbs

The effects of 24-h exposure to spectinomycin (100 microgram/ml) and ethidium bromide (1 microgram/ml) on the accumulation of chloroplast and mitochondrial rRNAs and on organelle ultrastructure were studied in greening cells of Ochromonas danica. Cells treated with ethidium bromide for 24 h divide at the same rate as controls but contain less than one third the normal amount of mitochondrial rRNA. Ultrastructural observations showed that these cells contain only 10% the number of mitochondrial ribosomes found in controls as well as fewer mitochondrial cristae. Ethidium bromide has no effect on chloroplast ultrastructure in Ochromonas. Greening cells treated with spectinomycin grow at close to control rates but contain 30–40% less chloroplast rRNA than do controls. Electron microscopy showed that spectinomycin disrupts the organization of chloroplast membranes and reduces the number of chloroplast ribosomes by 30%. Under these conditions, spectinomycin has no effect on mitochondrial rRNA or ultrastructure. Since spectinomycin is a specific inhibitor of translation on 70S ribosomes, these results are consistent with the possibility that at least some chloroplast ribosomal proteins are synthesized in the chloroplast of Ochromonas.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hauke S. Hillen ◽  
Elena Lavdovskaia ◽  
Franziska Nadler ◽  
Elisa Hanitsch ◽  
Andreas Linden ◽  
...  

AbstractRibosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.


Genetics ◽  
2020 ◽  
Vol 217 (2) ◽  
Author(s):  
Michael P McGurk ◽  
Anne-Marie Dion-Côté ◽  
Daniel A Barbash

AbstractDrosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85  Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.


Behaviour ◽  
1979 ◽  
Vol 70 (1-2) ◽  
pp. 1-116 ◽  
Author(s):  
I. Bossema

AbstractThe European jay (Garrulus g. glandarius) strongly depends on acorns for food. Many acorns are hoarded enabling the jay to feed upon them at times of the year in which they would otherwise be unavailable. Many of the hoarded acorns germinate and become seedlings so that jays play an important role in the dispersal of acorns and the reproduction of oaks (in this study: Quercus robur, the pedunculate oak). These mutual relationships were analysed both with wild jays in the field (province of Drente, The Netherlands) and with tame birds in confinement. Variation in the composition of the food throughout the year is described quantitatively. Acorns were the stock diet of adults in most months of the year. Leaf-eating caterpillars predominantly occurring on oak were the main food items of nestlings. Acorns formed the bulk of the food of fledglings in June. A high rate of acorn consumption in winter, spring and early summer becomes possible because individual jays hoard several thousands of acorns, mainly in October. In experiments, acorns of pedunculate oak were not preferred over equal sized acorns of sessile oak (which was not found in the study area). Acorns of pedunculate oak were strongly preferred over those of American oak and nuts of hazel and beech. Among acorns of pedunculate oak, ripe, sound, long-slim and big ones were preferred. Jays collect one or more (up to six) acorns per hoarding trip. In the latter case, the first ones are swallowed and the last one is usually carried in the bill. For swallowing the dimensions of the beak imposed a limit on size preference; for bill transport usually the biggest acorn was selected. The greater the number of acorns per trip, the longer was the transportation distance during hoarding. From trip to trip jays dispersed their acorns widely and when several acorns were transported during one trip, these were generally buried at different sites. Burial took place by pushing acorns in the soil and by subsequent hammering and covering. Jays often selected rather open sites, transitions in the vegetation and vertical structures such as saplings and tree trunks, for burial of acorns. In captivity jays also hoarded surplus food. Here, spacing out of burials was also observed; previously used sites usually being avoided. In addition, hiding along substrate edges and near conspicuous objects was observed. Jays tended to hide near sticks presented in a horizontal position rather than near identical ones in vertical position, especially when the colour of the sticks contrasted with the colour of the substrate. Also, rough surfaced substrate was strongly preferred over similar but smooth surfaced substrate. Successful retrieval of and feeding on hoarded acorns were observed in winter even when snow-cover had considerably altered the scenery. No evidence was obtained that acorns could be traced back by smell. Many indications were obtained that visual information from near and far beacons, memorized during hiding, was used in finding acorns. The use of beacons by captive jays was also studied. Experiments led to the conclusion that vertical beacons are more important to retrieving birds than identical horizontal ones. The discrepancy with the jay's preference for horizontal structures during hiding is discussed. Most seedlings emerge in May and June. The distribution pattern of seedlings and bill prints on the shells of their acorns indicated that many seedlings emerged from acorns hidden by jays in the previous autumn. The cotyledons of these plants remain underground and are in excellent condition in spring and early summer. Jays exploited acorns by pulling at the stem of seedlings and then removing the cotyledons. This did not usually damage the plants severely. Jays can find acorns in this situation partly because they remember where they buried acorns. In addition, it was shown that jays select seedlings of oak rather than ones of other species, and that they preferentially inspected those seedlings that were most profitable in terms of cotyledon yield and quality. Experiments uncovered some of the visual cues used in this discrimination. The effects of hoarding on the preservation of acorns were examined in the field and the laboratory. Being buried reduced the chance that acorns were robbed by conspecifics and other acorn feeders. Scatter hoarding did not lead to better protection of buried acorns than larder hoarding, but the spread of risk was better in the former than the latter. It was concluded that the way in which jays hoard acorns increases the chance that they can exploit them later. In addition, the condition of acorns is better preserved by being buried. An analysis was made of the consequences of the jay's behaviour for oaks. The oak does incur certain costs: some of its acorns are eaten by jays during the dispersal and storage phase, and some seedlings are damaged as a consequence of cotyledon removal. However, these costs are outweighed by the benefits the oak receives. Many of its most viable acorns are widely dispersed and buried at sites where the prospects for further development into mature oak are highly favourable. The adaptiveness of the characters involved in preferential feeding on and hoarding of acorns by jays is discussed in relation to several environmental pressures: competition with allied species; food fluctuations in the jay's niche; and food competitors better equipped to break up hard "dry" fruits. Reversely, jays exert several selective pressures which are likely to have evolutionary consequences for oaks, such as the selection of long-slim and large acorns with tight shells. In addition, oak seedlings with a long tap root and tough stem are selected for. Although other factors than mutual selective pressures between the two may have affected the present day fit between jays and oaks it is concluded that several characters of jays and oaks can be considered as co-adapted features of a symbiotic relationship.


1989 ◽  
Vol 9 (10) ◽  
pp. 4259-4264
Author(s):  
B L Seidel-Rogol ◽  
J King ◽  
H Bertrand

The natural-death mutant of Neurospora crassa has an accelerated senescence phenotype caused by a recessive mutation, nd, in a nuclear gene that is located in linkage group I. An examination of mitochondrial functions, however, revealed that the mutant has phenotypic and molecular defects similar to those commonly associated with maternally transmitted fungal senescence syndromes, including (i) deficiencies in cytochromes aa3 and b; (ii) a deficit in small subunits of mitochondrial ribosomes, and hence defective mitochondrial protein synthesis; and (iii) accumulation of gross rearrangements, including large deletions, in the mitochondrial chromosome of vegetatively propagated cells. These traits indicate that the nd+ allele codes for a function that is essential for stable maintenance of the mitochondrial chromosome, possibly a protein involved in replication, repair, or recombination.


1989 ◽  
Vol 9 (10) ◽  
pp. 4259-4264 ◽  
Author(s):  
B L Seidel-Rogol ◽  
J King ◽  
H Bertrand

The natural-death mutant of Neurospora crassa has an accelerated senescence phenotype caused by a recessive mutation, nd, in a nuclear gene that is located in linkage group I. An examination of mitochondrial functions, however, revealed that the mutant has phenotypic and molecular defects similar to those commonly associated with maternally transmitted fungal senescence syndromes, including (i) deficiencies in cytochromes aa3 and b; (ii) a deficit in small subunits of mitochondrial ribosomes, and hence defective mitochondrial protein synthesis; and (iii) accumulation of gross rearrangements, including large deletions, in the mitochondrial chromosome of vegetatively propagated cells. These traits indicate that the nd+ allele codes for a function that is essential for stable maintenance of the mitochondrial chromosome, possibly a protein involved in replication, repair, or recombination.


2021 ◽  
Author(s):  
Hauke S. Hillen ◽  
Elena Lavdovskaia ◽  
Franziska Nadler ◽  
Elisa Hanitsch ◽  
Andreas Linden ◽  
...  

Ribosome biogenesis is an essential process that requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. In particular, maturation of the peptidyl transferase center (PTC), the catalytic core of the ribosome, is mediated by universally conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial ribosomal large subunit (mtLSU) using a combination of endogenous complex purification, in vitro reconstitution and cryo-electron microscopy (cryo-EM). Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Subsequent addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch by releasing MTERF4-NSUN4 and GTPBP5 accompanied by the progression to a near-mature PTC state. In addition, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results define the molecular basis of dynamic GTPase-mediated PTC maturation during mitochondrial ribosome biogenesis and provide a framework for understanding step-wise progression of PTC folding as a critical quality control checkpoint in all translation systems.


Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2181
Author(s):  
Ivan Laptev ◽  
Olga Dontsova ◽  
Petr Sergiev

Modified nucleotides are present in all ribosomal RNA molecules. Mitochondrial ribosomes are unique to have a set of methylated residues that includes universally conserved ones, those that could be found either in bacterial or in archaeal/eukaryotic cytosolic ribosomes and those that are present exclusively in mitochondria. A single pseudouridine within the mt-rRNA is located in the peptidyltransferase center at a position similar to that in bacteria. After recent completion of the list of enzymes responsible for the modification of mammalian mitochondrial rRNA it became possible to summarize an evolutionary history, functional role of mt-rRNA modification enzymes and an interplay of the mt-rRNA modification and mitoribosome assembly process, which is a goal of this review.


2020 ◽  
Author(s):  
Emma B. Hodcroft ◽  
Robert Dyrdak ◽  
Cristina Andrés ◽  
Adrian Egli ◽  
Josiane Reist ◽  
...  

BackgroundWorldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease.MethodsWe collected samples from several European countries during the 2018 out-break and determined 53 near full-length genome (‘whole genome’) sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences.FindingsIn 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly.InterpretationWe hypothesize that EV-D68’s rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults.FundingUniversity of Basel and Swedish Foundation for Research and Development in Medical Microbiology


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