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Bulat Tretyakov
Bulat Tretyakov

Ep 818 - Google Drive ^NEW^



You may have noticed construction going on at our Paseo location, 1216 Paseo de Oñate, in Española. We are excited to announce that we have added Interactive Teller Machines to increase speed and convenience in our drive-through! Learn more here.




Ep 818 - Google Drive



This Week: Kevin kicks off the show with a John Wick drive-by on the box office, then he talks about the arrest of Jonathan Majors and what that means for his movies. Next, he looks at trailers for Asteroid City and Elemental. Later, he reviews Dungeons & Dragons: Honor Among Thieves, Tetris, The Big Door Prize and Buck Rogers in the 25th Century. Finally, he wraps things up with the Home-Cinema Round-Up with a spotlight on Dead Silence on 4K and Deemo: Memorial Keys.


So to continue evaluating this urban legend, we can skip on down a bit. The next thing it claims is that later European wagons used this same width because if they were going to drive in the Roman ruts with a non-conforming axle width, it would have "broken their wheels". It's true that if you needed a wagon to travel a particular route, and that route is on an old Roman road with artificial ruts, you'd do better to match that width to get a smoother, more efficient ride. But what we've already learned is that those ruts were not all the same size, and also that rutted sections of road were fragmented and inconsistent. Wagons built to any given specification would have found benefit only on a few scattered, noncontiguous sections of road.


Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.


A large lateral gene transfer event in the last common ancestor (LCA) of AOA is proposed to have played a major role in their transition to a chemolithoautotrophic lifestyle12,15. However, there is currently little evidence for other cases of large lateral gene acquisition in Thaumarchaeota evolution16,17, and little is known of the relative contributions of gene duplications and genes losses. Large-scale events of lateral gene transfer (LGT) have been suggested as major drivers of proteome evolution in diverse archaeal lineages18, including Thaumarchaeota16. However, the long evolutionary history of Thaumarchaeota (>2.3 billion years of evolution) and their diversification in a range of ecosystems2,12,14 raises the possibility that distinct evolutionary mechanisms have shaped thaumarchaeotal genomes across their history. In particular, we hypothesise that an ongoing process of LGT spread across thaumarchaeotal evolution (in contrast, or addition to acquisitions at their origin) was the major source of molecular innovation. Phylogenomic methods based on reconstructed ancestral gene contents have been used previously throughout the archaeal radiation to explicitly model gene family acquisitions, duplications and losses using a recently-developed approach for probabilistic gene mapping19 by amalgamated likelihood estimation (ALE)20. However, the aforementioned study only included a limited number of Thaumarchaeota. Similarly, a recent comparative analysis of a diverse set of thaumarchaeotal genomes examining the influence of oxygen availability on diversification did not include the large diversity of terrestrial thaumarchaeotal genomes presented here, nor disentangle the contributions of gene transfer and gene duplication to genomic diversification15.


Kdp, a high-affinity ATP-driven potassium uptake system that enables K+-mediated osmoregulation in potassium limited environments36, is present in several Nitrososphaerales genomes, but almost completely absent from marine Thaumarchaeota (with the exception of REDSEA-S19-B12N3). In the event of osmotic shock, this system could allow the organisms to maintain turgor pressure in soils where there is low potassium concentration or where potassium is bound to negatively charged humus or clay particles by cation exchange.


The exhaustive creation of probabilistic ancestral reconstructions from every branch of the thaumarchaeotal phylogeny allowed the characterisation and quantification of proteome changes along every lineage (Fig. 3 and Supplementary Fig. 5; Supplementary Data 4). The majority of the predicted 67,400 gene content gains in Thaumarchaeota evolution occurred through 51,653 duplications (77% of gains) of pre-existing genes, with 11,430 intra-phylum gene transfers (intra-LGT) (17% of gains) and 4317 originations (including inter-phyla gene transfers (inter-LGT) and de novo gene formation) (6% of gains). There were also 227,837 gene losses predicted, indicating gene duplication and gene loss as the two most significant drivers of gene content change in Thaumarchaeota evolution. The same ancestral genes were lost along multiple lineages, explaining the higher number (nearly 3.5-fold) of losses than gains.


The transition from AOA LCA to the last common ancestor of Nitrosocaldales (NC LCA) involved several functional gains, including geranylgeranylglycerol-phosphate geranylgeranyltransferase (EC:2.5.1.42), which is involved in the formation of polar membrane lipids in many thermophilic archaea, and the vitamin-B12-independent methionine synthase (EC:2.1.1.14), functionally replacing the vitamin-B12-dependent methionine synthase (EC:2.1.1.13), which is absent from every member of this order. The DNA polymerase D (EC:2.7.7.7) was also lost in NC LCA. Both the presence of vitamin-B12-independent methionine synthase and the absence of DNA polymerase D were previously reported in Ca. N. islandicus 3F42 and Ca. N. cavascurensis SCU243, but present results expand those findings to all members of the order. Other notable losses in this transition are the Kdp, high-affinity ATP-driven K+-transport system (EC:3.6.3.12), which is involved in osmotic stress resistance in low potassium environments and Uvr excinuclease, which is involved in DNA repair from ultraviolet DNA damage. Kpd is absent from almost all marine Thaumarchaeota in this analysis, indicating that this system is not essential in this environment. It has been proposed that the absence of Uvr in deep-water Nitrosopumilales is due to the lack of light in this environment12. This theory agrees with the absence of these genes in Nitrosocaldales, which derive from hot spring (in the case of 3F, SCU2 and J079) and deep ocean (in the case of SAT137 and UBA231) environments in which light is also likely limited.


It has been proposed that archaeal genome evolution is driven by punctuated episodes of extensive gene acquisition, followed by lineage-specific gene loss48. While our analysis indicates that gene transfer contributed to the evolution of Nitrososphaerales, the predominant mode of genome expansion was gene duplication of both ancestral and originating gene families, with higher duplication rates occurring in the latter. As suggested previously49, the duplication of newly acquired genes by LGT may facilitate higher gene dosage of a novel metabolic function, which can enable increased production of a gene product in high demand50. Duplicated genes can diverge sufficiently to perform a novel function51,52,53 (neofunctionalisation) or specialise to perform the same function under different environmental conditions, such as pH54 or temperature55 (subfunctionalisation). Therefore, duplication may have a role in Nitrososphaerales adaptation, allowing the maintenance of essential functions in fluctuating and heterogeneous terrestrial environments56. While gene duplication has been previously reported in archaea and bacteria, its importance in comparison to LGT may have been underappreciated, at least for some lineages49. This unexpected importance of duplication in the evolution of Nitrososphaerales led us to reinterpret the results of a previously archaea-wide evolutionary analysis19, which revealed that a similar pattern of large origination events (>500 gene families) and subsequent duplications (>350 duplications) may have also occurred in other archaeal lineages, especially for the lineages with the largest known archaeal genomes (including Haloarcula marismortui and Haloferax volcanii)19. Taken together, these results suggest that duplication of ancestrally acquired genes may be an important mechanism of genome expansion across a number of archaeal lineages. Larger genome sizes have been reported for mesophilic soil prokaryotes (both archaea and bacteria) compared to marine relatives57, but it is unclear whether this is due to genome expansion in soil lineages from ancestors with smaller genomes, or from genome reduction in marine lineages. This work provides an example of a case in which soil-marine genome size differences are driven by genome expansion in soil lineages. While gene duplication is a well-documented mechanism in eukaryotic evolution58, demonstration of its importance in thaumarchaeotal evolution requires further investigation across other microbial lineages. 041b061a72


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