Table 2 Predictions to better differentiate inside-out and outside-in models

Two prokaryotic genomes (nuclear and mitochondrial) contributed to the ancestral eukaryotic genome.

Two prokaryotic genomes (nuclear and mitochondrial) contributed to the ancestral eukaryotic genome.

Three prokaryotic genomes (nuclear, cytoplasmic, and mitochondrial) contributed to the ancestral eukaryotic genome.

Mitochondria or mitochondrially derived genes are present in all eukaryotes.

Eukaryotes might be found that have no evidence of having mitochondria in their ancestry.

Eukaryotes might be found that have no evidence of having mitochondria in their ancestry.

The perinuclear space contains machinery (for example, N-linked glycosylation) similar to that used to modify the archaeal cell wall.

Homologs of archaeal cell wall proteins, if present, are found on the surface of eukaryotes rather than in the perinuclear space.

The perinuclear space contains machinery related to host food vacuole functions or the cell wall of the endosymbiont lineage.

LINC proteins are homologous to proteins anchoring the archaeal plasma membrane and/or cortical cytoskeleton to the cell wall. Homologs of glycosylated SUN proteins are present in archaeal cell walls.

LINC proteins are likely derived from proteins that function in controlling the shape of membrane-bound vesicles or ER cisternae.

Inner LINC proteins are derived from the periphery of the endosymbiont lineage, outer LINC proteins from the food vacuole of the host lineage.

Homologs of structural nucleoporins are localized to the plasma membrane of eocytes and play a role in stabilizing extracellular projections.

Homologs of structural nucleoporins play a role in invagination of the archaeal plasma membrane.

Homologs of structural nucleoporins play a role in regulated transport into and out of food vacuoles in the host and/or form secretion systems in the endosymbionts.

Nucleoporins form a paraphyletic grade from which COPII-like proteins evolved.

Nucleoporins are embedded in a paraphyletic grade composed of COPII-like proteins that are involved in endosomal trafficking.

Nucleoporins form a paraphyletic grade from which COPII-like proteins evolved.

Synthesis of eukaryotic phospholipids and sterols is accomplished by genes of α-proteobacterial ancestry.

Synthesis of eukaryotic phospholipids and sterols is accomplished by genes of eukaryotic ancestry or by archaeal genes plus genes acquired laterally from bacteria other than mitochondria.

Synthesis of eukaryotic phospholipids and sterols is accomplished by genes of host and endosymbiont ancestry, but not mitochondria.

New interphase nuclear pores are inserted from inside the nucleus at the neck of outward projections from the inner surface of the nuclear membrane.

New interphase nuclear pores are inserted from both inside and outside the nucleus and induce the fusion of inner and outer nuclear membranes to generate a pore.

New nuclear pores arise either from the outside, by host-derived proteins, or from the inside by endosymbiont-derived proteins. No prediction is made as to how they puncture inner and outer membranes.

ER is largely continuous, even in syncytia generated by the suppression of cell division.

ER is largely discontinuous in the absence of ER fusion machinery.

ER is continuous by virtue of deriving from and connecting to the nuclear envelope.

Cytoplasmic continuity must be actively maintained. The cytoplasm associated with individual nuclear pores will show signs of limited connectivity when rates of cytoplasmic fusion are low.

Cytoplasm tends to be continuous.

Cytoplasm tends to be continuous.

Nuclei can, in general, retain distinct domains of action in the context of a syncytium.

Nuclei in syncytia exert local control of adjacent cytoplasm only through recently evolved specialized mechanisms.

Nuclei in syncytia exert local control of adjacent cytoplasm only through recently evolved specialized mechanisms.

Protein functions related to anterograde secretion will tend to be ancestral to functions related to endocytosis, phagocytosis, and retrograde transport.

Proteins functions related to retrograde vesicle trafficking and endocytosis will tend to be ancestral to functions related to anterograde transport and secretion.

Proteins functions related to phagocytosis will tend to be ancestral to functions related to anterograde transport and secretion.

Eukaryotes might be found that retain the ancestral condition of transient connections between ER and the cell's exterior, or in which there is anterograde but not retrograde vesicle transport.

Eukaryotes might be found that retain the ancestral condition of having a nuclear envelope that is not fully assembled, or that lacks nuclear pores, or in which there is endocytosis but no exocytosis, or in which there in retrograde but not anterograde vesicle transport.

No intermediates will be found.

Transitions between open and closed mitosis are easy and accomplished by changing the stability of LINC complexes and the extent to which nuclear membranes are released into bulk ER by nuclear pore disassembly.

Transitions from open mitosis (the ancestral state) to closed mitosis are difficult to achieve and require the de novo evolution of machinery for nuclear fission.

Transitions from closed mitosis (the ancestral state) to open mitosis are very difficult and require rupture and reassembly of the endosymbiont plasma membrane and host food vacuole membrane.

Closed mitosis will utilize ESCRTIII in a manner similar to archaeal cell division.

Closed mitosis will utilize eukaryote-specific molecular mechanisms.

Closed mitosis will utilize molecular mechanisms acquired from the endosymbiont.

The segregation of ER at cell division in a closed mitosis is primarily accomplished by the segregation of nuclear-pore associated cytoplasmic domains.

The segregation of ER at cell division in a closed mitosis is tightly regulated with scission events actively separating domains of ER.

The segregation of ER at cell division in a closed mitosis is tightly regulated with scission events actively separating domains of ER.

Cell cycle control will be dominated by nuclear events, with secondary controls acting to coordinate nuclear and cytoplasmic events.

Cell cycle control may be dominated by cytoplasmic events, with secondary controls acting to coordinate nuclear and cytoplasmic events.

There may be entirely separate mechanisms governing cell cycle control within the nucleus and cytoplasm.

Flagella may utilize proteins homologous to those involved in nuclear pore formation and trafficking.

Flagella formation need not involve proteins like those involved in nuclear pore formation.

Flagella formation need not involve proteins like those involved in nuclear pore formation.