Abstract:Endopeptidase classification based on catalytic mechanism and evolutionary history has proven to be invaluable to the study of proteolytic enzymes. Such general mechanistic- and evolutionary- based groupings have launched experimental investigations, because knowledge gained for one family member tends to apply to the other closely related enzymes. The serine endopeptidases represent one of the most abundant and diverse groups, with their apparently successful proteolytic mechanism having arisen independently … Show more
“…Reciprocal BLAST analysis and secondary structure similarities detected by HHPred38 indicate that two of the proteins, termed TimRhom I and TimRhom II, belong to the rhomboid family of proteins. This protein family consists of not only intramembrane proteases that are conserved in all domains of life3940 but also includes a growing group of rhomboid-like proteins that are proteolytically inactive41. TimRhom I and TimRhom II belong to the latter group, since the Ser-His catalytic dyad is not conserved (Supplementary Fig.…”
Section: Resultsmentioning
confidence: 99%
“…The situation for the presequence translocase of T. brucei is quite different, since, besides TbTim17, its essential core includes the rhomboid-like proteins TimRhom I and TimRhom II. Rhomboid-like proteins are found in all three domains of life including α-proteobacteria40. Since TimRhom I and TimRhom II are not closer related to eukaryotic rhomboid-like proteins (for example, derlins, PARL) than to their bacterial counterparts, they may have been commandeered from the original endosymbiont that gave rise to mitochondria.…”
Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.
“…Reciprocal BLAST analysis and secondary structure similarities detected by HHPred38 indicate that two of the proteins, termed TimRhom I and TimRhom II, belong to the rhomboid family of proteins. This protein family consists of not only intramembrane proteases that are conserved in all domains of life3940 but also includes a growing group of rhomboid-like proteins that are proteolytically inactive41. TimRhom I and TimRhom II belong to the latter group, since the Ser-His catalytic dyad is not conserved (Supplementary Fig.…”
Section: Resultsmentioning
confidence: 99%
“…The situation for the presequence translocase of T. brucei is quite different, since, besides TbTim17, its essential core includes the rhomboid-like proteins TimRhom I and TimRhom II. Rhomboid-like proteins are found in all three domains of life including α-proteobacteria40. Since TimRhom I and TimRhom II are not closer related to eukaryotic rhomboid-like proteins (for example, derlins, PARL) than to their bacterial counterparts, they may have been commandeered from the original endosymbiont that gave rise to mitochondria.…”
Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.
“…It has been suggested that the bacterial rhomboids with the 6 + 1 TM helices could either be a bacterial progenitor to the eukaryotic rhomboid proteases or they may represent an ancient family of rhomboid proteases present in the last universal common ancestor (LUCA) [45]. The fact that family A (6 + 1 TM topology) and family D (6 TM topology) are present in all genomes analyzed suggests that each family could have different and potentially critical biological roles in Streptomyces .Figure 3Transmembrane structure of Rhomboids using TMRPres2D [45]. Rhomboids a , b , c and d are from S. coelicolor , and e is from S. sviceus active sites are highlighted with a red circle.…”
BackgroundProteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are present in all forms of life and their function is not fully understood, although some evidence suggests they participate in cell signaling. Streptomycetes are prolific soil bacteria with diverse physiological and metabolic properties that respond to signals from other cells and from the environment. In the present study, we investigate the evolutionary dynamics of rhomboids in Streptomycetes, as this can shed light into the possible involvement of rhomboids in the complex lifestyles of these bacteria.ResultsAnalysis of Streptomyces genomes revealed that they harbor up to five divergent putative rhomboid genes (arbitrarily labeled families A–E), two of which are orthologous to rhomboids previously described in Mycobacteria. Characterization of each of these rhomboid families reveals that each group is distinctive, and has its own evolutionary history. Two of the Streptomyces rhomboid families are highly conserved across all analyzed genomes suggesting they are essential. At least one family has been horizontally transferred, while others have been lost in several genomes. Additionally, the transcription of the four rhomboid genes identified in Streptomyces coelicolor, the model organism of this genus, was verified by reverse transcription.ConclusionsUsing phylogenetic and genomic analysis, this study demonstrates the existence of five distinct families of rhomboid genes in Streptomycetes. Families A and D are present in all nine species analyzed indicating a potentially important role for these genes. The four rhomboids present in S. coelicolor are transcribed suggesting they could participate in cellular metabolism. Future studies are needed to provide insight into the involvement of rhomboids in Streptomyces physiology. We are currently constructing knock out (KO) mutants for each of the rhomboid genes from S. coelicolor and will compare the phenotypes of the KOs to the wild type strain.
“…Finally, Kinch and Grishin take us back to the beginning by reconsidering rhomboid protease evolution [24]. Intramembrane proteases are nearly ubiquitous enzymes across all life forms, presenting a wealth of biological settings for analysis, yet complicating evolutionary interpretations.…”
The turn of the millennium coincided with the branding of a fundamentally different class of enzyme - proteases that reside immersed inside the membrane. This new field was the convergence of completely separate lines of research focused on cholesterol homeostasis, Alzheimer's disease, and developmental genetics. None intended their ultimate path, but soon became a richly-integrated fabric for an entirely new field: regulated intramembrane proteolysis. Our aim in this Special Issue is to focus on the ancient and nearly ubiquitous enzymes that catalyze this unexpected yet important reaction. The pace of progress has been dramatic, resulting in a rapidly-expanding universe of known cellular functions, and a paradigm shift in the biochemical understanding of these once heretical enzymes. More recently, the first therapeutic successes have been attained by targeting an intramembrane protease. We consider these advances and identify oncoming opportunities in four parts: growing spectra of cellular roles, insights into biochemical mechanisms, therapeutic strategies, and newly-emerging topics. Recent studies also expose challenges for the future, including non-linear relationships between substrate identification and physiological functions, and the need for potent and specific, not broad-class, inhibitors.
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