Commentary: Manifold Routes to a Nucleus

Jogler, Christian; Wiegand, Sandra; Devos, Damien P.

doi:10.3389/fmicb.2019.01198

Cited by 4 publications

(8 citation statements)

References 31 publications

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“…We also observed pores in previous cell wall preparations of T. immobilis (Mahajan et al, 2020a). We therefore favor the hypothesis that the pore-containing membrane corresponds to the outer membrane, an interpretation that has also been suggested by others (Jogler et al, 2019).…”

Section: Discussionsupporting

confidence: 90%

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns

et al. 2021

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The Planctomycetes bacteria have unique cell architectures with heavily invaginated membranes as confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. The subcellular proteome of T. immobilis was examined by differential solubilization followed by LC-MS/MS analysis, which identified 1569 proteins in total. The Tris-soluble fraction contained mostly cytoplasmic proteins, while inner and outer membrane proteins were found in the Triton X-100 and SDS-soluble fractions, respectively. For comparisons, the subcellular proteome of Escherichia coli was also examined using the same methodology. A notable difference in the overall fractionation pattern of the two species was a fivefold higher number of predicted cytoplasmic proteins in the SDS-soluble fraction in T. immobilis. One category of such proteins is represented by innovations in the Planctomycetes lineage, including unique sets of serine/threonine kinases and extracytoplasmic sigma factors with WD40 repeat domains for which no homologs are present in E. coli. Other such proteins are members of recently expanded protein families in which the newly evolved paralog with a new domain structure is recovered from the SDS-soluble fraction, while other paralogs may have similar domain structures and fractionation patterns as the single homolog in E. coli. The expanded protein families in T. immobilis include enzymes involved in replication-repair processes as well as in rRNA and tRNA modification and degradation. These results show that paralogization and domain shuffling have yielded new proteins with distinct fractionation characteristics. Understanding the molecular intricacies of these adaptive changes might aid in the development of a model for the evolution of cellular complexity.

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Section: Discussionsupporting

confidence: 90%

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns

et al. 2021

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“…This structure was originally postulated to uncouple transcription machinery from translation of mRNA in the cell cytoplasm ( Fuerst, 2005 ). More recent work suggests that ribosomes are found within the Planctomycetes nucleus-like structure ( Fuerst, 2005 ; Hendrickson and Poole, 2018 ; Jogler et al, 2019 ). It has been proposed that there is a larger proportion of active ribosomes distributed distantly from the nucleoid than adjacent to it ( Gottshall et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

The Phage Nucleus and PhuZ Spindle: Defining Features of the Subcellular Organization and Speciation of Nucleus-Forming Jumbo Phages

2021

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Bacteriophages and their bacterial hosts are ancient organisms that have been co-evolving for billions of years. Some jumbo phages, those with a genome size larger than 200 kilobases, have recently been discovered to establish complex subcellular organization during replication. Here, we review our current understanding of jumbo phages that form a nucleus-like structure, or “Phage Nucleus,” during replication. The phage nucleus is made of a proteinaceous shell that surrounds replicating phage DNA and imparts a unique subcellular organization that is temporally and spatially controlled within bacterial host cells by a phage-encoded tubulin (PhuZ)-based spindle. This subcellular architecture serves as a replication factory for jumbo Pseudomonas phages and provides a selective advantage when these replicate in some host strains. Throughout the lytic cycle, the phage nucleus compartmentalizes proteins according to function and protects the phage genome from host defense mechanisms. Early during infection, the PhuZ spindle positions the newly formed phage nucleus at midcell and, later in the infection cycle, the spindle rotates the nucleus while delivering capsids and distributing them uniformly on the nuclear surface, where they dock for DNA packaging. During the co-infection of two different nucleus-forming jumbo phages in a bacterial cell, the phage nucleus establishes Subcellular Genetic Isolation that limits the potential for viral genetic exchange by physically separating co-infection genomes, and the PhuZ spindle causes Virogenesis Incompatibility, whereby interacting components from two diverging phages negatively affect phage reproduction. Thus, the phage nucleus and PhuZ spindle are defining cell biological structures that serve roles in both the life cycle of nucleus-forming jumbo phages and phage speciation.

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“…In addition, other publications have reported features of G. obscuriglobus that are normally associated with eukaryotes, including endocytosis-like processes (Lonhienne et al, 2010), the separation of transcription and translation (Gottshall et al, 2014), and the presence of structures that resemble the nuclear pore complex (Sagulenko et al, 2017). We acknowledged that the issue of whether there is a nucleus-like compartment in Gemmata and related bacteria is a “matter of ongoing debate” and respectfully disagree with Jogler and colleagues' conclusion (Jogler et al, 2019) that this possibility has been disproven. For example, while one electron tomography study (Acehan et al, 2014) using plastic embedding concluded that G. obscuriglobus is neither compartmentalized or nucleated, a subsequent cryo-electron tomography study from an independent group (Sagulenko et al, 2014) supported compartmentalization.…”

mentioning

confidence: 82%

“…Jogler et al (2019) recently published a commentary in response to our paper in which they took no issue with any of the key points of our paper. Instead, they criticized the way we discussed results concerning the fascinating bacterium, Gemmata obscuriglobus , and cited additional references, mostly from their own labs.…”

mentioning

confidence: 94%

“…For example, while one electron tomography study (Acehan et al, 2014) using plastic embedding concluded that G. obscuriglobus is neither compartmentalized or nucleated, a subsequent cryo-electron tomography study from an independent group (Sagulenko et al, 2014) supported compartmentalization. Similarly, Jogler and colleagues' claim (Jogler et al, 2019) that structures from the internal membrane of Gemmata that resemble the eukaryote nuclear pore complex (Sagulenko et al, 2017) are instead crateriform structures found on the exterior of G. obscuriglobus cannot account for the observations that proteins associated with these pores are exclusive to inner membranes (Sagulenko et al, 2017), and that antibodies raised against them are both specific and localized exclusively to the inner membranes. The field is still working toward a full characterization and understanding of the unusual membrane architecture (and associated biology) of Gemmata so it is premature to refer to a paradigm shift as having taken place.…”

mentioning

confidence: 99%

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