Abstract
BackgroundThe nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system.ResultsIn this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families.ConclusionThe results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis.
Highlights
The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes
The genomic exploration of nuclear location signals (NLSs)-like motifs in species of family Planctomycetaceae provided us with insights into possible genomic changes contributing to the evolution of NLS and nuclear membranes
We focused on NLS-bearing proteins in 11 strains of the family Planctomycetaceae using comparative genomic approaches
Summary
The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. This marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Planctomycetaceae are taxonomically affiliated with bacteria, they have been in past studies reported to possess a number of characteristics that are closer to eukaryotes, especially the absence of peptidoglycan in their cell envelope, synthesis of. Arguing on the other hand in favor of potential homology is the finding that ICMs divide cells of all examined planctomycete species into two compartments, the paryphoplasm and pirellulosome [16, 17], and may make transcription and translation independent, allowing for the development of eukaryotic cellular complexity [18]. Exploration of unusual molecular features that may contribute to or be a consequence of the complicated internal features of family Planctomycetaceae is urgent
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