New insights about major transitions on the tree of life

New insights about major transitions on the tree of life

The last Virtual problem from Genomology and evolution highlights articles that provide new insight into the deep evolutionary relationships between existing organisms and the origin of eukaryotes from archaeal lines. All cellular organisms are descended from a shared ancestor, often called LUCA – the last universal common ancestor. Relationships between these organisms can be depicted by an evolutionary network known as the “tree of life”, which in recent decades has included three main forms of life – bacteria, archaea and eukaryotes. Evolutionary biologists have long sought to understand the location of LUCA within this framework, as well as the origins of LECA – the last eukaryotic common ancestor. Unfortunately, it is a great challenge to correctly conclude the relationship between microbial lines due to the large evolutionary distances involved, as well as the frequent lateral transfer of genetic material between lines. Recently, however, new data and methods have resulted in profound changes in our understanding of the tree of life.

The headline of this virtual issue is a review by Anja Spang, Tara A. Mahendrarajah, Pierre Offre and Courtney W. Stairs entitled “Developing perspectives on the origin and diversification of cellular life and the virosphere”(Spang et al. 2022). Their article summarizes the latest findings on LUCA and LECA, as well as the potential role of the virus in the development of both prokaryotes and eukaryotes. According to Spang, the authors are “fascinated by the concept of the tree of life because it has so much explanatory power, not only to describe the existing diversity of life and its relationship but also to help understand the evolution of the genome through time from LUCA. We therefore considered a a review that integrates the various major discoveries regarding organism and viral diversity as well as important evolutionary transitions would be very valuable. ” In particular, the decision to include viruses in the discussion provides a somewhat unique perspective. According to co-author Mahendrarajah, “Viruses have rarely been discussed in reviews of the trees of life, and we felt they would be a good complement to our perspective given their important roles in gene sharing. between cellular life and the implications for organism development. ”

Several previously published studies in this area focus on identifying key traits that distinguish bacteria and archaea and try to deduce their origin in the LUCA context. For example, bacteria and archaea have different cell membrane phospholipids synthesized by non-homologous enzymes, and Coleman et al. (2019) showed that LUCA was likely to have the ability to synthesize archeal-type membrane phospholipids. Bacteria and archaea also differ in their histone proteins, although relatively little is known about archaeal histone proteins. Stevens et al. (2022) showed that the two histones found in the model archaeon Thermococcus kodakarensis are preserved at least above the order Thermococcales and also revealed the presence of highly divergent histone-folding proteins related to bacterial histones in several Thermococcales genomes. The origins of nitrogenases, nitrogen-fixing enzymes found in both bacteria and archaea, have also puzzled many researchers; a recent study by Garcia et al. (2022) showed that nitrogenases may have evolved from maturases, homologues that today participate in nitrogenase cofactors, rather than the other way around. This raises new questions about the environmental factors that led to the emergence of this critical biogeochemical innovation.

Another primary focus in the area is the position of LUCA in relation to existing bacteria and archaea. Although it is generally believed that the root of the tree of life lies between archaea and bacteria, it is difficult to formally exclude alternatives due to the potential for phylogenetic artifacts. In addition, the root of the archaea and in particular the location of the various DPANN archaea (an abbreviation based on the first five groups discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), which represent many lines of symbiotic and small genome members. , is still uncertain (Spang et al., 2022). It is especially challenging to accurately place symbionts in phylogenetic trees, partly because they can exchange genes with their hosts and often experience faster evolutionary speeds, which in turn can confuse tree-building methods. For example, Feng et al. (2021) showed that some individual gene trees grouped one of the DPANN lines, Nanohaloarchaea, with Haloarchaea, rather than with other DPANN taxa. Despite this, they found that most large linked data sets were consistent with the monophony of DPANN superphyllum in unrooted phylogenies, highlighting the difficulty of correctly concluding deep relationships between these lines. Although various concatenated gene tree findings suggest that DPANN forms a monophyletic draft, it remains to be assessed whether they are monophyletic and deeply branched in rooted trees (Spang et al., 2022).

An additional key issue concerns the origin of eukaryotes and the location of LECA on the tree. A symbiogenetic origin of eukaryotes has long been suspected, in which an archeal cell acquired a bacterial endosymbiont, resulting in a proto-eukaryote containing a proto-mitochondrion. According to Tria et al. (2021), evidence from gene duplications in LECA supports this early origin of mitochondria, and reveals serial copying of bacterial genes from the proto-mitochondria to the genome of the archaeal host. This may partly explain why a study by Brueckner and Martin (2020) found that eukaryotic genome generally has more bacterial genes than archaeal genes, with bacteria contributing 53% of the genes in eukaryotic lines without plastids and 61% in photosynthetic eukaryotic lines.

As described in detail in Spang et al. (2022) review, phylogenetic analyzes have recently suggested that the closest archaeal sister line to eukaryotes may be Asgard archaea, a proposed superphylum consisting of Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota. As further evidence for this, Penev et al. (2020) discovered that the large ribosomal subunit (LSU) rRNA from Lokiarchaeota and Heimdallarchaeota bridges the gap in size between prokaryotic and eukaryotic LSU rRNAs. However, this phylogenetic grouping remains somewhat controversial due to the fact that the vast majority of Asgard sequences come from metagenomic composites (MAGs), which can suffer from data analysis artifacts that can result in false findings. A study by Garg et al. (2021) suggested that some Asgard archaic MAGs may be unnatural structures resulting from the assembly or binding processes. Yet this is controversial (Spang et al. 2022), and the first genome of a cultured member of Lokiarchaeota (Imachi et al., 2019) has confirmed the ubiquitous presence of eukaryotic signature proteins in the Asgard archaea.

Further research has focused on early eukaryotic evolution and features dating back to LECA, with many studies showing that LECA already had a relatively high degree of eukaryotic complexity. This includes several proteins and protein complexes involved in cellular processes that are thought to be unique to eukaryotes. For example, Vargová et al. (2021) revealed that LECA had as many as 16 ARF GTPases, proteins that play a role in eukaryotic-specific processes such as membrane trade, tubulin assembly, actin dynamics, and cilia-related functions. Similarly, Yoshinaga and Inagaki (2021) found that LECA probably had two distinct SMC proteins, which are crucial for successful chromosome replication and segregation, while Santana-Molina et al. (2021) showed that LECA already had a CATCHR protein complex involved in vesicle trade. A critical question is whether such features may have originated in the archaeological lineage of the ancestor before eukaryogenesis. Knopp et al. (2021) found that only 0.3% of the protein families found in LECA can be attributed to the Asgard archaea, which casts doubt on the idea that the archaic ancestral lineage developed many of these traits before eukaryogenesis. Examining another aspect of LECA, Skejo et al. (2021) excitedly suggested that LECA may have been multinucleated, pointing to common relationships between polynuclear forms across eukaryotic supergroups. If true, this would fundamentally change our understanding of the evolutionary transitions among early eukaryotes.

Spang et al. (2022) proposes a number of ways to further promote our understanding of the tree of life and solve the unanswered questions that remain. According to co-author Stairs, progress to date has been “made possible by major technological advances in sequencing and bioinformatics, pioneering in the microbiological and medical fields. higher levels of sequence divergence than their prokaryotic counterparts. ” Other critical areas for exploration include increasing the amount of sequence data available across the tree of life, developing new phylogenetic and phylogenetic methods to resolve incongruences and uncertainties, reconstructing ancestral sequences and by using cell biology to link genotypes to phenotypes and better understand proteins. structures and cellular properties. Co-author Offre believes that such methodological approaches are necessary for “further progress in our understanding of the tree of life in the coming years”, which ultimately leads to “an integrative view of life’s biological diversity and its evolution.”

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