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Background: The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty.

According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism.

Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the longstanding assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex sex overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results: I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages sex two initial stages origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility.

Then octagonal nuclear pore complexes NPCs arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages.

These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex.

I also explain why many alternative ideas are inadequate. Conclusion: Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins.

The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others. In bacteria the typically single and circular DNA chromosome is attached to the surface cyto-plasmic membrane and unijenie by protein motors. Eukaryote chromosomes are normally multiple and linear and never attach directly to the surface plasma membrane.

Instead they are fixed to and surrounded by a specialised part of the endomembrane system the nuclear envelope, NE during interphase, the part of the cell cycle when the cell grows, genes are transcribed, and DNA replicated. During cell division, by contrast, eukaryotic chromosomes are compacted. The problem of nuclear origins therefore requires understanding coevo-lution of about 27 cell components Appendix 1 and how they became functionally interlinked into the fundamentally novel eukaryotic life cycle [], approximately My ago, at least two unijenie years after bacteria evolved [6].

Not only mitosis, but also sex, i. This conclusion follows irrespective of whether the eukaryote tree is between unikonts animals, fungi and three protozoan phyla and bikonts plants, chromists and all other protozoan phyla [7,8] or is instead between Euglenozoa and all other eukaryotes as shown in Fig.

Peroxisomes, mitochondria, cen-trioles, cilia, and Golgi dictyosomes must also have originated prior to the last common ancestor of all extant eukaryotes, whichever of these unijenie of the root is correct [6]. This radical transformation of cell structure eukaryogenesis is the most complex and extensive case of quantum evolution in the history of life [2,3,6].

Beforehand earth was a sexless, purely bacterial and viral world. Afterwards sexy, endoskeletal eukaryotes evolved morphological complexity: diatoms, butterflies, corals, whales, kelps, and trees. Evolution of complex characters typically involves pre-adaptation, radical mutational innovation, and different selective forces acting in succession [3,6,10]. Here I paint an integrated picture of how the nucleus, sex, and the eukaryotic cell cycle originated and congealed into a novel, unified, and very conservative cellular lifestyle during later stages of unijenie conversion of a bacterium into a eukaryote.

In addition to establishing the phylogenetic context Fig. As first argued 30 years ago [11], origin of the cell nucleus cannot be understood in isolation from other major innovations of the eukaryotic cell; intracellular coevolution among different cell constituents that interact physically or that profoundly affect selective forces acting on each other is the key to understanding eukaryote origins [3,4].

Elements of the present synthesis were presented then [11], e. However, the phylogenetic context has changed dramatically with our now much more robust understanding of cell phylogeny 1 [3,7,8,12,13]. Moreover, genomics has enabled molecular origins of many key eukaryotic constituents, including NPCs, to be traced [], whilst advances in molecular cell biology tell us how nuclei actually assemble [18,19] and function.

Building on these insights, I now propose the first specific physical mechanism for evolving nuclear envelope architecture and explain its major genetic unijenie and why other theories are inadequate. As the field of eukaryogenesis has been confused by a plethora of contradictory ideas, some not compatible with established evidence, before presenting the novel explanations I summarise two areas to put them in context: 1 the phylogenetic origin of the eukaryotic components, and 2 the origin of the endomembrane system and cytoskeleton.

I only outline the conclusions, giving references for details, as most of the evidence and arguments is not new, being already published. Because the nature of molecular changes during major evolutionary transitions is more diversified and complex than some molecular evolutionists have realised, I also preface my original explanations of the origin of the nucleus with an outline of some basic but widely neglected evolutionary principles that apply to all such major innovations in body plan.

This background is rather long because the proper evolutionary context is so important: the nucleus did not evolve on its own; explanations of its origin make no sense without understanding the prior evolution of the endomembrane system of which its envelope is a specialised part.

Intracellular coevolution of about a novel properties is at the core of understanding eukaryogenesis. Eukaryote cells are all evolutionary chimaeras of an ancestrally phagotrophic host cell with nucleus, endo-membranes, and endoskeleton [3] and an enslaved a-proteobacterium converted into a mitochondrion close to the time when the nucleus itself originated, i. Contrary to some assumptions [17,21], the host for that symbiogenesis was not an archaebacterium, but an otherwise fully developed early eukaryote with NE and cilium a protoeukaryote or else an intermediate stage prekaryote that had already evolved rudiments of phagocytosis the likely means of engulfing the a-proteo-bacterium and internal membranes already differentiated into a primitive ER and peroxisomes, endoskeleton, centrosomes and mitosis see [3,6,20,22] for further explanation.

Figure 1 The tree of life and major steps in cell evolution. Archaebacteria are sisters to eukaryotes and, contrary sex widespread assumptions, the youngest bacterialphylum [6,13]. This tree topology, coupled with extensive losses of posibacterialproperties by the ancestral archaebacterium, explains without lateralgene transfer how eukaryotes possess a unique combination of properties now seen in archaebacteria, posibacteria and a-proteobacteria.

Eukaryote origins in three stages indicated by asterisks probably immediately followed divergence of archaebacteria and eukaryote precursors from the ancestralneomuran.

This ancestor arose from a stem actinobacterial posibacterium by a quantum evolutionary shake-up of bacterialorganization - sex neomuran revolution [6,12]: surface N-linked glycoproteins replaced murein; ribosomes evolved the signalrecognition particle's translationalarrest domain; sex replaced DNA gyrase, radically changing DNA replication, repair, and transcription enzymes. The eukaryote depicted is a hypotheticalearly stage after the origin of nucleus, mitochondrion, cilium, and microtubular skeleton but before distinct anterior and posterior cilia and centriolar and ciliary transformation anterior cilium young, posterior old: [3] evolved probably in the cenancestraleukaryote [9].

Kingdom Chromista was recently expanded sex include not only the originalgroups Heterokonta, Cryptista and Haptophyta, but also Alveolata, Rhizaria and Heliozoa [9], making the name chromalveolates now unnecessary. Excavata sex exclude Euglenozoa and comprise just three phyla: the ancestrally aerobic Percolozoa and Loukozoa and the ancestrally anaerobic Metamonada e. Giardia, Trichomonaswhich evolved from an aerobic Malawimonas-related loukozoan. Sterols and phosphatidylinositol PI probably evolved in the ancestral stem actinobacterium but the ancestralhyperthermophilic archaebacterium lost them when isoprenoid ethers replaced acylester lipids.

Figure 1 differs from many widely discussed views of the tree of life in three major respects: the position of the root of the whole tree, the position of the eukaryotic root, and in the idea that both archaebacteria and eukar-yotes evolved from Posibacteria. Though these topics are explained in detail in other papers, many readers may not have assimilated the evidence therein that rather strongly supports them, so I shall begin by outlining the evidence for these interpretations and add a few novel arguments and new evidence for them and explain the flaws in alternative ideas on the rooting and topology of the tree.

Archaebacteria are clearly related to the eukaryote host together forming a clade called neomura [4,12]. But there is no sound evidence that archaebacteria are directly ancestral to eukaryotes.

Instead several arguments show they are their sisters [6,12,13]. N-linked glycoproteins, more complex RNA polymerases, core histones are not specifically archaebacterial, but neomuran characters that evolved in their common ancestor during the neomuran revolution [4,6,12,13].

Purely archaebacterial characters notably unique isoprenoid ether lipids and flagella evolved in the ancestral archaebacterium after it diverged from the prekaryote lineage [12,13]. Moreover, genes shared by eukaryotes and eubacteria, but not archaebacteria e.

MreB that became actin [3,6], and eubacterial surface molecules that became NE lamin B receptors [14], and enzymes making acyl ester phospholipidswere probably lost by the ancestral archaebacterium, which apparently underwent massive gene loss during its secondary sex to hyperther-mophily [12,13].

In addition to those earlier arguments, the most comprehensive multigene analysis to date convincingly places archaebacteria as a holophyletic clade that is sister to eukaryotes, not ancestral to them [24]. However, these authors confusingly refer to the 'deep archaeal origin of eukaryotes' despite their strong evidence that all extant archaebacteria form a derived clade not a paraphyletic ancestral group. The phrase unijenie origin' wrongly implies that the common ancestor of eukaryotes and archaebacteria had the specific positive attributes of archaebacteria that distinguish them from both eukaryotes and eubacteria, of which there are very few: notably the isoprenoid ether lipids, archaeosine modified rRNAs, flagella, and duplicate versions of DNA polymerase B [25].

It is unparsimonious to assume that such characters were present in and then lost by the ancestors of eukar-yotes. Though the replacement of archaebacterial lipids by acyl ester lipids derived from the enslaved proteobac-terial ancestor of mitochondria is a formal possibility [26], it would be evolutionarily extremely onerous and thus unlikely, and phylogeny gives no convincing reason to assume it in the first place.

Moreover, the hypothesis of replacement by archaebacterial lipids by eubacterial lipids from the a-proteobacterial symbiont totally fails to explain the origin of phosphatidylinositol, which played a key role in eukaryogenesis [27] and sex present in all the actinobacterial relatives of neomura but never in archaebacteria or proteobacteria.

Thus, it is far more likely that both archaebacteria and eukaryotes evolved from a common ancestor that was a prokaryote with acyl ester lipids including phosphatidylinositol, but which had not yet evolved either the specifically archae-bacterial properties like isoprenoid ether lipids or any eukaryotic properties.

Sterol evolution even more strongly refutes the idea that eukaryotes evolved from archaebacteria and independently shows that neomura are most closely related to actinobacteria.

Sterols in actinobacteria and eukar-yotes are synthesised from squalene, as are the hopa-noids of eubacteria. In unijenie posibacteria squalene is produced from isopentenyl diphosphate IPPwhich is also the precursor for the isoprenoid tails of archaebac-terial lipids; in posibacteria, archaebacteria, and eukar-yotes that never have plastids which use instead the cyanobacterial DOX isoprenoid pathway IPP is generated by the mevalonate synthetic pathway, the enzymes of which were clearly in place and inherited vertically from the last common ancestor of Posibacteria and neo-mura [28,29].

As the enzymes that convert IPP into ster-ols are entirely absent from archaebacteria and mostly absent from a-proteobacteria, this simultaneously refutes the popular but totally erroneous ideas that archaebacteria were directly ancestral to eukaryotes [26,30,31] and that eukaryotes got sterols from the enslaved mitochondrion [26,]. Actinobacteria are the only bacteria in which many genes needed for making sterols are phylogenetically widespread and of ancient origin within the group. Sequence trees for four major enzymes of sterol synthesis refute the idea that any of these genes entered actinobacteria by lateral gene transfer [34] and are totally consistent with the vertical descent of sterol biosynthesis from an actinobacterium-like posibacterium to the first eukaryote and their loss in the ancestral archaebacterium when replacement of acyl esters by isoprenoid ethers provided an alternative and superior means of making membranes more rigid.

Oddly, though recognising that their trees rule out lateral transfer from eukaryotes to actinobacteria. Desmond and Gribaldo [34] evade the obvious conclusion that Posibacteria were indeed ancestral to neomura by postulating lateral transfer LGT of these genes from a stem pre-eukaryotic lineage into actinobacteria, despite there being no evidence whatever for that implausible and unparsimonious scenario, which would require that Actinobacteria are younger than pre-eukaryotes.

The first enzyme of sterol synthesis for squalene monooxy-genation making squalene epoxide is so widespread in actinobacteria that it must have been present in their last common ancestor [34]; elsewhere in prokaryotes it is known only from a few gamma and delta proteobac-teria and one planctomycete all members of the clade Gracilicutes [13] ; as the trees do not require any LGT it probably evolved in the last common ancestor of Posi-bacteria and Gracilicutes after the prior divergence of Cyanobacteria and the oxygenation of the atmosphere; it is entirely absent from archaebacteria and a-proteobac-teria.

As sterol synthesis requires oxygen its loss by secondarily or facultatively anaerobic lineages is unsurprising the likelihood that the ancestral archae-bacterium was largely anaerobic [12] is another reason why it lost sterols. The tree suggests that one plancto-bacterium Stigmatella replaced its own enzyme by one from eukaryotes, but gives no evidence for LGTs amongst eubacteria, contrary to the authors assumption [34].

Such replacement by LGT of one enzyme within a pathway is mechanistically simple, but there is no evidence for LGT of the whole pathway at any time in the history of life by contrast symbiogenetic replacement by whole cell enslavement did allow the mevalonate part of the pathway to be replaced by that of cyanobacteria.

The third enzyme in the pathway that catalyses C14 demethylation of lanosterol is known only from the order Actinomycetales widespread within Actinobac-teria and from one delta and one gamma proteobacter-ium; as the tree does not support the idea of LGT, most likely it evolved at the same time as the first enzyme but was lost or evolved beyond bioinformatic recognition more often.

The enzyme DHCR24, which unijenie the more complex sterols ergosterol and cholesterol, is present widely and phylogenetically deeply in Actinomyce-tales within Actinobacteria and is sister to its eukaryotic. Homologues were detected in only one other bacterium: Methylococcus; its sequence branches well within opisthokonts and was therefore probably acquired by LGT from an animal; however there is no evidence for LGT for that gene provided one roots the tree correctly. The simplest interpretation of the alternative lanosterol and cycloartenol pathways in eukaryotes [35] is that the first eukaryote inherited the posibacterial oxidosqualene cyclase vertically and that it was mutationally modified in plants at the time of origin of plastids and to make cycloartenol preferentially and later transferred to other eukaryotes by secondary symbiogenesis i.

Thus sterol and phosphatidylinositol evolution independently refute the idea that eukaryotes evolved from archaebacteria and both strongly indicate that the closest relatives to neomura are actinobacteria in agreement with a dozen other characters [12]. However, the evolution of archaebacterial lipids and neomuran glyco-proteins suggests that neomura may have evolved from the other posibacterial subphylum, Endobacteria.

Homologues of the glycosyl transferases that make N-linked glycoproteins were detectable only in Endobacteria among eubacteria [13] and geranylgeranylglyceryl phosphate synthase GGGPS the enzyme that attaches iso-prenoid tails to sn-GlycerolP to make the membrane lipids of archaebacteria is known only from Endobac-teria specifically Bacillales and the sphingobacterium Cytophaga, making it likely that Endobacteria rather than Actinobacteria were ancestral to neomura.

This evidence for an endobacterial origin of neomura can be readily reconciled with the more extensive evidence for their actinobacterial affinities by the posibacterial tree topology of Fig.

We need only postulate that the cenancestral acti-nobacterium lost glycosyl unijenie and GGGPS after it diverged from neomura and that phosphatidylinositol evolved immediately prior to that bifurcation and was lost only by archaebacteria together with other acyl esters. This topology also allows the extra 5' Alu domain of the neomuran signal recognition 7SL RNA to have been inherited directly from Endobacteria [12], making it unnecessary to postulate that the positionally equivalent domain present in some Endobacteria alone among eubacteria is convergent [13] - assuming that 5'.

As previously discussed [13], the other key enzyme for the archaebacterial replacement of eubacterial lipids, sn-gly-cerolphosphate dehydrogenase, which makes their unique sn-glycerolphosphate, almost certainly evolved from a known posibacterial homologue also present in Thermotoga and Proteobacteria [28,29].

The idea that archaebacterial lipids evolved independently of eubacter-ial biosynthetic pathways and the idea that their cells evolved independently of eubacterial cells [36,37] are both utter nonsense. If actinobacteria are holophyletic Fig. However, one would have to assume that the most divergent actinobacterial branches had lost 20S proteasomes, as they are restricted to Actinomycetales [13].

Skophammer et al. A quaternary structure argument for dihydroorotate hydrogenase PyrD evolution [41] supports a common ancestry for archaebacteria and Endobacteria; but that does not mean that they alone form a clade, for we all accept that the ancestral eukaryote was cladistically closer to Archaebacteria than Endobacteria, so it must have lost the PyrD 1B paralogue; an additional loss by the ancestral actinobacterium reconciles their argument with Fig.

An indel argument to exclude the root of the tree of life from Actinobacteria [42] actually excludes it only from the orders Actinomycetales and Bifidobacteriales, as their analysis included no DNA gyr-ase GyrA proteins from the three most deeply branching orders. But that limitation of the argument does not matter, as there was never any reason to think the root was within Actinobacteria in the first place.

My own alignment indicates that the only available GyrA from the deepest branching actinobacterium Rubrobacter does not have the four amino acid insertion found in other actinobacteria, suggesting that it evolved after the first internal divergence, possibly substantially later incidentally the insertion region seems incorrectly aligned in [42] and the gap should probably be moved by five amino acids.

One cannot use this indel to argue against the topology or rooting of Fig. A eukaryote-specific topoisomerase IIA probably also evolved from DNA gyrase by fusion of GyrA and GyrB to make a chimaera also so different from its eubacterial ancestors that one cannot apply the indel argument to it. Given the ancestral neomuran transformations of gyrase into novel topoisomerases, the very few archaebacterial GyrAs that can be aligned with those of eubacteria almost certainly entered archaebac-teria by LGT from eubacteria [43], so the absence in them of the higher actinobacterial 4-amino acid insertion [42] must not be used to argue against actinobacteria being sisters of neomura Fig.

The above arguments from eukaryote and archaebac-terial lipid evolution strongly contradict and are more compelling than a recent gene analysis in which, in contrast to standard phylogenetic methods that show archaebacteria as holophyletic sisters of eukaryotes, a theoretically superior heterogeneous method shows archaebacteria as paraphyletic ancestors to eukaryotes.

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