Core Proteome of the Minimal Cell: Comparative Proteomics of Three Mollicute Species

Abstract

Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with an extremely small genome size and very limited coding capacity. Thus, they may serve as a model of a ‘minimal cell’: a cell with the lowest possible number of genes yet capable of autonomous self-replication. We present the results of a comparative analysis of proteomes of three mycoplasma species: A. laidlawii, M. gallisepticum, and M. mobile. The core proteome components found in the three mycoplasma species are involved in fundamental cellular processes which are necessary for the free living of cells. They include replication, transcription, translation, and minimal metabolism. The members of the proteome core seem to be tightly interconnected with a number of interactions forming core interactome whether or not additional species-specific proteins are located on the periphery. We also obtained a genome core of the respective organisms and compared it with the proteome core. It was found that the genome core encodes 73 more proteins than the proteome core. Apart of proteins which may not be identified due to technical limitations, there are 24 proteins that seem to not be expressed under the optimal conditions.

Systems Biology Perspectives on Minimal and Simpler Cells

“…Building on results of another study of the interactome of M. pneumoniae (45), those authors also concluded that most COGs in the Mollicutes core proteome-140 -are expected to associate in protein complexes, and 54 COGs are predicted to participate in more than one complex (43). Due to secondary functions of such complexes, such as the maintenance of overall cellular stability (and particularly genome stability), which could explain the maintenance of incomplete metabolic pathways in reduced genomes, those authors proposed that the concept of a minimal genome should be treated not as a set of essential functions but as a set of essential structures (43).…”

“…In another work, the proteomes of Acholeplasma laidlawii and Mycoplasma gallisepticum were analyzed by two-dimensional (2D) electrophoresis, matrix-assisted laser desorption ionization (MALDI), and liquid chromatography-mass spectrometry (LC-MS) (43) and compared to the proteome of Mycoplasma mobile obtained in another study (44). Clusters of orthologous genes (COGs) were used to compare both the genomes and proteomes of the three Mollicutes species (43). Two hundred twelve COGs were identified as being part of the core proteome, including DNA replication, repair, transcription, and translation and molecular chaperones.…”

“…Two hundred twelve COGs were identified as being part of the core proteome, including DNA replication, repair, transcription, and translation and molecular chaperones. Some metabolic pathways were also represented in this core proteome, including glycolysis, the nonoxidative part of the pentose phosphate pathway, glycerophospholipid biosynthesis, and the synthesis of nucleoside triphosphates (43). One surprising finding was the low level of conservation of proteins related to cell division, as only two proteins were conserved in the core: FtsH and an Smc-like protein.…”

“…One surprising finding was the low level of conservation of proteins related to cell division, as only two proteins were conserved in the core: FtsH and an Smc-like protein. Strikingly, the genome of M. mobile does not even contain FtsK or FtsZ, which indicates that the essential process of cell division has greater plasticity than other cellular systems (43). Building on results of another study of the interactome of M. pneumoniae (45), those authors also concluded that most COGs in the Mollicutes core proteome-140 -are expected to associate in protein complexes, and 54 COGs are predicted to participate in more than one complex (43).…”

Divided we stand: splitting synthetic cells for their proliferation

“…Second, in spite of the high conservation of many division proteins, and in contrast to some other core cellular machineries like translation or transcription, the division system exhibits a high level of redundancy and plasticity. For example, a comparison the genomes of three different Mollicutes bacteria species, known for their reduced genomes, has identified only two cell-division proteins that are common to all three species (Fisunov et al 2011). Hence, multiple realizations can probably be found to address the question of how to divide simple synthetic cells.…”