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

Abstract

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.

Linking prokaryotic genome size variation to metabolic potential and environment

“…It has been previously observed that Planctomycetota is the phylum containing the aquatic MAG with the biggest known estimated genome size (14.93 Mbp) [ 2 ]. These large genomes contain large collections of genes that could be linked to the very complex cell structures and chromosomes observed in this phylum [ 36 ]. Still, further research is necessary to understand if extant genome size in phylum Plactomycetota is the result of ecological adaptation to abiotic gradients.…”

Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles

“…Biological triplicates of fractions DGUC F3 and F6 from A. kunkeei strains A1401 and A0901 were subjected for proteomics analysis after in-solution digestion, essentially as described previously (Seeger et al 2021 ). Notably, for the F6 samples that contained a high concentration of proteins, 10 μg of proteins was used for the digestion (ca 10 μl of the sample).…”

“…Extracted proteins of the WCL and CFP fractions were analyzed by Label-free quantification (LFQ) by LC-MS/MS as described previously (Seeger et al 2021 ). For the LFQ analyses, MS raw files were processed using MaxQuant software (Cox and Mann 2008 ) and the Andromeda search engine (Cox et al 2011 ) against the genome sequences of A. kunkeei A0901 and A1401.…”

Unravelling evolution one nucleotide at a time

“…Even though bacterial cells generally do not contain internal compartments, there are exceptions, like bacteria of the Planctomycetes phylum that contain a proteinaceous cell wall and an invaginated inner membrane (Mahajan et al 2020 ). In Tuwongella immobilis , Siv and her team visualised a complex tunnel system made by the invaginations thus resulting in an increased periplasmic space (Seeger et al 2021 ). While the function of this extended compartment is not fully understood yet, it is hypothesised that the bacterium uses the periplasm for storage and degradation of imported macromolecules.…”