Structural and Functional Insights into
            <i>Aeropyrum pernix</i>
            OppA, a Member of a Novel Archaeal OppA Subfamily

Balestrieri, Marco; Gogliettino, Marta; Fiume, Immacolata; Pocsfalvi, Gabriella; Catara, Giuliana; Rossi, Mosè; Palmieri, Gianna

doi:10.1128/jb.00899-10

Cited by 6 publications

(5 citation statements)

References 36 publications

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“…The difference in sequence could mean that the proteins have different oligopeptide ligands. Oppa is usually lipid anchored in the membrane, but studies have reported that a soluble form actively binds peptides in the cytosol of other organisms ( 26 ). Our collaborators have previously noted that Methanococcus voltae (a close cousin to M. barkeri ) cells grown on FeS 2 show increased biofilm formation and clumping ( 14 ), and the proteomes of Fe(II)/HS − - and FeS 2 -grown M. barkeri have upregulated proteins related to biofilm formation and signaling.…”

Section: Resultsmentioning

confidence: 99%

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

Fausset,

Spietz,

Cox

et al. 2024

Microbiol Spectr

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Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS − ). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS 2 ). Recently, paradigm-shifting studies indicate that Fe and S in FeS 2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS 2 , as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS 2 , Fe(II)/HS − , or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS − , either as a component of the growth medium [Fe(II)/HS − ] or generated through reduction of FeS 2 , were likely a major factor underpinning these phenotypic differences. IMPORTANCE The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

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Section: Resultsmentioning

confidence: 99%

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

Fausset,

Spietz,

Cox

et al. 2024

Microbiol Spectr

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“…Then, the solution was mixed with the peptide bradykinin (RPPGFSPFR) and crystallized in order to elucidate interactions with the specific peptide rather than endogenous peptides. Bradykinin was used in peptide selectivity studies of other archaeal OppAs 16,17 …”

Section: Resultsmentioning

confidence: 99%

“…Bradykinin was used in peptide selectivity studies of other archaeal OppAs. 16,17 The structure determination by the molecular replacement method using the structure of B. subtilis OppA (PDB ID: 1XOC) 25 was unsuccessful due to low sequence identity of 14%. Structure determination by multi-wavelength anomalous dispersion or singlewavelength anomalous dispersion (SAD) methods using selenomethionine (SeMet) derivative protein was unsuccessful because most of the methionine residues may be located in the loop region according to secondary-structure prediction.…”

Section: Structure Determination Of Tkoppamentioning

confidence: 99%

“…Based on a genomic survey of Pyrococcus species, archaeal Opps consist of five components similarly to bacterial ones 3 . Archaeal OppA was first isolated and characterized from the extracellular medium of Aeropyrum pernix 15 and functionally characterized by assays of peptide binding and selectivity using OppAs of A. pernix 16 and Sulfolobus solfataricus 17 . There are several reports that archaea produce membrane vesicles.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for peptide recognition by archaeal oligopeptide permease A

et al. 2022

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Oligopeptide permease A (OppA) plays an important role in the nutrition of cells and various signaling processes. In archaea, OppA is a major protein present in membrane vesicles of Thermococcales. Because there being no crystal structures of archaeal OppAs determined to date, we report the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA) at 2.3 Å resolution by the single‐wavelength anomalous dispersion method. TkOppA consists of three domains similarly to bacterial OppAs, and the inserted regions not present in bacterial OppAs are at the periphery of the core region. An endogenous pentapeptide was bound in the pocket of domains I and III of TkOppA by hydrogen bonds of main‐chain atoms of the peptide and hydrophobic interactions. No hydrogen bonds of side‐chain atoms of the peptide were observed; thus, TkOppA may have low peptide selectivity but some preference for residues 2 and 3. TkOppA has a relatively large pocket and can bind a nonapeptide; therefore, it is suitable for the binding of large peptides similarly to OppAs of Gram‐positive bacteria.

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“…The class of oligopeptide-binding proteins characterized in the crenarchaeal species S. solfataricus and Aeropyrum pernix contains an N-terminal secretory signal sequence with an SPase I cleavage site and an additional C-terminal transmembrane segment (Elferink et al, 2001 ; Gogliettino et al, 2010 ; Balestrieri et al, 2011 ). The membrane anchor is preceded by a stretch of glycosylated serine and threonine residues.…”

Section: Diversity Of Secreted Proteinsmentioning

confidence: 99%

Diversity and Subcellular Distribution of Archaeal Secreted Proteins

Szabó

Pohlschröder

2012

Front. Microbio.

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Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.

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Structural and Functional Insights into Aeropyrum pernix OppA, a Member of a Novel Archaeal OppA Subfamily

Cited by 6 publications

References 36 publications

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

Structural basis for peptide recognition by archaeal oligopeptide permease A

Diversity and Subcellular Distribution of Archaeal Secreted Proteins

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