Cell surface proteins in archaeal and bacterial genomes comprising “LVIVD”, “RIVW” and “LGxL” tandem sequence repeats are predicted to fold as β-propeller

Adindla, S.; Inampudi, Krishna Kishore; Guruprasad, Lalitha

doi:10.1016/j.ijbiomac.2007.06.004

Cited by 9 publications

(8 citation statements)

References 56 publications

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“…Previously, it was already shown, that at least four non-integrin type of 7-bladed β-propeller domains as well as several 8-, 6- and 4-bladed β-propeller domains were found in bacteria [29], [30]. Herein we present strong evidence that bacterial sequences encode structures that are equivalent to the 7-bladed β-propeller found in human integrins.…”

Section: Introductionsupporting

confidence: 54%

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

et al. 2011

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Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and sometimes two tandem copies are found.

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Section: Introductionsupporting

confidence: 54%

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

et al. 2011

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“…Of the predicted “surface-resident” proteins, only one (MA0336) was detected, albeit only when lower stringency (without SDS) washes was employed. In a subsequent study, Adindla, et al predicted 23 M. acetivorans and 16 M. mazei proteins as surface-resident based on their novel sequence repeats 53,54. None of those proteins were observed in our in vivo labeling experiments.…”

Section: Discussionmentioning

confidence: 59%

S-layer, Surface-Accessible, and Concanavalin A Binding Proteins of Methanosarcina acetivorans and Methanosarcina mazei

et al. 2009

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The outermost cell envelope structure of many archaea and bacteria contains a proteinaceous lattice termed the surface layer or S-layer. It is typically composed of only one or two abundant, often posttranslationally modified proteins that self-assemble to form the highly organized arrays. Surprisingly, over a hundred proteins were annotated to be S-layer components in the archaeal species Methanosarcina acetivorans C2A and Methanosarcina mazei Gö1, reflecting limitations of current predictions. An in vivo biotinylation methodology was devised to affinity tag surface-exposed proteins while overcoming unique challenges in working with these fragile organisms. Cells were adapted to growth under N 2 fixing conditions, thus minimizing free amines reactive to the NHSlabel, and high pH media compatible with the acylation chemistry was used. A 3-phase separation procedure was employed to isolate intact, labeled cells from lysed-cell derived proteins. Streptavidin affinity enrichment followed by stringent wash conditions removed non-specifically bound proteins. This methodology revealed S-layer proteins in M. acetivorans C2A and M. mazei Gö1 to be MA0829 and MM1976, respectively. Each was demonstrated to exist as multiple glycosylated forms using SDS-PAGE coupled with glycoprotein-specific staining, and by interaction with the lectin, Concanavalin A. A number of additional surface-exposed proteins and glycoproteins were identified and included all three subunits of the thermosome: the latter suggests that the chaperonin complex is both surface-and cytoplasmically-localized. This approach provides an alternative strategy to study surface proteins in the archaea.

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“…The Hvo_0405 region N-terminal to the PGF motif contains a predicted Tat signal peptide and several LVIVD repeat domains ( Fig. 1A), which are predicted to form a four-␤-stranded ␤-propeller domain that is often found in archaeal and bacterial proteins that localize to the cell surface (19,20). The Hvo_0405 region C-terminal to the PGF motif contains a conserved NifU-like domain; originally discovered in proteins involved in nitrogen fixation, proteins containing a NifU-like domain are found in many species and typically bind a 4Fe-4S cluster ( Fig.…”

Section: Resultsmentioning

confidence: 99%

ArtA-Dependent Processing of a Tat Substrate Containing a Conserved Tripartite Structure That Is Not Localized at the C Terminus

et al. 2017

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Most prokaryote-secreted proteins are transported to the cell surface using either the general secretion (Sec) or twin-arginine translocation (Tat) pathway. A majority of secreted proteins are anchored to the cell surface, while the remainder are released into the extracellular environment. The anchored surface proteins play a variety of important roles in cellular processes, ranging from facilitating interactions between cells to maintaining cell stability. The extensively studied S-layer glycoprotein (SLG) of , previously thought to be anchored via C-terminal intercalation into the membrane, was recently shown to be lipidated and to have its C-terminal segment removed in processes dependent upon archaeosortase A (ArtA), a recently discovered enzyme. While SLG is a Sec substrate, analyses presented here reveal that, of eight additional ArtA substrates predicted, two substrates also contain predicted Tat signal peptides, including Hvo_0405, which has a highly conserved tripartite structure that lies closer to the center of the protein than to its C terminus, unlike other predicted ArtA substrates identified to date. We demonstrate that, even given its atypical location, this tripartite structure, which likely resulted from the fusion of genes encoding an ArtA substrate and a cytoplasmic protein, is processed in an ArtA-dependent manner. Using an Hvo_0405 mutant lacking the conserved "twin" arginines of the predicted Tat signal peptide, we show that Hvo_0405 is indeed a Tat substrate and that ArtA substrates include both Sec and Tat substrates. Finally, we confirmed the Tat-dependent localization and signal peptidase I (SPase I) cleavage site of Hvo_0405 using mass spectrometry. The specific mechanisms that facilitate protein anchoring to the archaeal cell surface remain poorly understood. Here, we have shown that the proteins bound to the cell surface of the model archaeon , through a recently discovered novel ArtA-dependent anchoring mechanism, are more structurally diverse than was previously known. Specifically, our results demonstrate that both Tat and Sec substrates, which contain the conserved tripartite structure of predicted ArtA substrates, can be processed in an ArtA-dependent manner and that the tripartite structure need not lie near the C terminus for this processing to occur. These data improve our understanding of archaeal cell biology and are invaluable for subcellular localization predictions of archaeal and bacterial proteins.

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Cell surface proteins in archaeal and bacterial genomes comprising “LVIVD”, “RIVW” and “LGxL” tandem sequence repeats are predicted to fold as β-propeller

Cited by 9 publications

References 56 publications

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

S-layer, Surface-Accessible, and Concanavalin A Binding Proteins of Methanosarcina acetivorans and Methanosarcina mazei

ArtA-Dependent Processing of a Tat Substrate Containing a Conserved Tripartite Structure That Is Not Localized at the C Terminus

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