Proteome profiling of the green sulfur bacterium <i>Chlorobaculum tepidum</i> by N‐terminal proteomics

Kouyianou, Kalliopi; Bock, Pieter-Jan De; Nikolaki, Antigoni; Aktoudianaki, Aikaterini; Gevaert, Kris; Tsiotis, Georgios

doi:10.1002/pmic.201000739

Cited by 10 publications

(13 citation statements)

References 22 publications

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“…Although Kouyianou et al. noticed that iMet excision in Chlorobaculum tepidum is lower compared than in other organisms and organelles, they also observed partial iMet excision for 8% of the identified proteins (23 distinct proteins) and complete iMet excision for 34% of the proteins (104 proteins). Similar results were obtained in Coxiella burnetti (6% for partial iMet excision and 46% for total iMet excision).…”

Section: Resultsmentioning

confidence: 93%

Proteome‐wide analysis of the amino terminal status of Escherichia coli proteins at the steady‐state and upon deformylation inhibition

2015

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A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions, more than 1000 unique N-termini were identified with 56% showing initiator methionine removal. Additional modifications corresponded to partial or complete Nα-acetylation (10%) and N-formyl retention (5%). Among the proteins undergoing these N-terminal modifications, 140 unique N-termini from translocated membrane proteins were highlighted. The very early time-course impact of actinonin was followed after addition of bacteriostatic concentrations of the drug. Under these conditions, 26% of all proteins did not undergo deformylation any longer after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation ratio measured on individual proteins increased with the same trend. Upon early PDF inhibition, two major categories of proteins retained their N-formyl group: a large number of inner membrane proteins and many proteins involved in protein synthesis including factors assisting the nascent chains in early cotranslational events. All MS data have been deposited in the ProteomeXchange with identifiers PXD001979, PXD002012 and PXD001983 (http://proteomecentral.proteomexchange.org/dataset/PXD001979, http://proteomecentral.proteomexchange.org/dataset/PXD002012 and http://proteomecentral.proteomexchange.org/dataset/PXD001983).

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Section: Resultsmentioning

confidence: 93%

Proteome‐wide analysis of the amino terminal status of Escherichia coli proteins at the steady‐state and upon deformylation inhibition

2015

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“…As observed in chromatophores (Fig. 2), many of these N-termini are generated by cleavage C-terminal to arginine (or asparagine) residues and create N-termini starting with threonine or serine (Kouyianou et al, 2012;Rowland et al, 2015;Berry et al, 2017) proteoforms. Further known mechanisms for the generation of functional proteoforms from one pre-protein are for example N-terminal trimming of several amino acids by exo-or endopeptidases, zymogen activation via cleavage of a pro-peptide, etc.…”

Section: Discussionmentioning

confidence: 94%

“…S2A ). Although in cyanobacteria, N-terminal threonine, valine, serine, and alanine can be acetylated following iMet excision (Bonissone et al, 2013), the overall frequency of N-terminal acetylation is low in bacteria (<5 %; Soppa 2010; Kouyianou et al, 2012; Yang et al, 2014; Schmidt et al, 2016), but much higher for plastid-encoded proteins (Giglione and Meinnel, 2001; Huesgen et al, 2013; Rowland et al, 2015). Hence, the frequency of N-acetylation in the chromatophore is more comparable to plastids, suggesting the involvement of host-derived factors in this process.…”

Section: Discussionmentioning

confidence: 99%

A bipartite chromatophore targeting peptide and N-terminal processing of proteins in the Paulinella chromatophore

Oberleitner

Perrar

Macorano

et al. 2021

Preprint

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The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles - termed chromatophores - that evolved from a cyanobacterium ~100 million years ago, independently from plastids in plants and algae. Despite its more recent origin, at least one third of the chromatophore proteome consists of nucleus-encoded proteins that are imported by an unknown mechanism across the chromatophore double envelope membranes. Chromatophore-targeted proteins fall into two classes. Proteins exceeding 250 amino acids carry a conserved N-terminal sequence extension, termed the 'chromatophore transit peptide' (crTP), that is presumably involved in guiding these proteins into the chromatophore. Short imported proteins do not carry discernable targeting signals. To explore whether the import of protein is accompanied by their N-terminal processing, here we used a mass spectrometry-based approach to determine protein N-termini in Paulinella chromatophora and identified N-termini of 208 chromatophore-localized proteins. Our study revealed extensive N-terminal modifications by acetylation and proteolytic processing in both, the nucleus and chromatophore-encoded fraction of the chromatophore proteome. Mature N-termini of 37 crTP-carrying proteins were identified, of which 30 were cleaved in a common processing region. Our results imply that the crTP mediates trafficking through the Golgi, is bipartite and surprisingly only the N-terminal third ('part 1') becomes cleaved upon import, whereas the rest ('part 2') remains at the mature proteins. In contrast, short imported proteins remain largely unprocessed. Finally, this work sheds light on N-terminal processing of proteins encoded in an evolutionary-early-stage photosynthetic organelle and suggests host-derived post-translationally acting factors involved in dynamic regulation of the chromatophore-encoded chromatophore proteome.

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“…The degradomes of 10 eubacterial species (75–83) and at least three archaeal species (84–86) have been studied. These studies include two human pathogens ( N. meningitidis and Coxiella burnetii , which causes Q fever) but are not limited to pathogens, also including model bacterial organisms.…”

Section: Microbial Degradomicsmentioning

confidence: 99%

Sharpening Host Defenses during Infection: Proteases Cut to the Chase

Marshall

Finlay

Overall

2017

Molecular & Cellular Proteomics

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The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.

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Proteome profiling of the green sulfur bacterium Chlorobaculum tepidum by N‐terminal proteomics

Cited by 10 publications

References 22 publications

Proteome‐wide analysis of the amino terminal status of Escherichia coli proteins at the steady‐state and upon deformylation inhibition

Proteome‐wide analysis of the amino terminal status of Escherichia coli proteins at the steady‐state and upon deformylation inhibition

A bipartite chromatophore targeting peptide and N-terminal processing of proteins in the Paulinella chromatophore

Sharpening Host Defenses during Infection: Proteases Cut to the Chase

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