DING proteins are from Pseudomonas

DING proteins have been described as animal and plant proteins with potential biomineralisation, receptor or signalling roles that have been characterised by an N-terminal DINGGG-sequence. However, these sequences have only ever been identified as either N-terminal peptides or partial cDNA sequences, and have yet to be detected in any of the many genomic animal and plant genomes now available. Microbial relatives of the DING proteins have been described, which appear to be periplasmic phosphate-binding proteins. Recently, full-length Pseudomonas aeruginosa UCBPP-PA14 and Hypericum perforatum genes have been sequenced that show high homology to the published DING protein N-terminal sequences, and small peptides previously identified in conjunction with the peptide sequencing of DING proteins can also be mapped to regions across these full-length sequences. Searching with these sequences identifies other plant and animal cDNA fragments in the public nucleotide databases, and, additionally, an unordered rat genomic contig that contains a DING-like sequence on a small fragment. Analysing the codon usage of these DNA sequences identifies all of these sequences as of Pseudomonas origin, suggesting that DING proteins do not exist in eukaryotes, but instead are potentially due to microbial contamination or infection.     

The DING family of proteins: ubiquitous in eukaryotes,but where are the genes?

PstS and DING proteins are members of a superfamily of secreted, high‐affinity phosphate‐binding proteins. Whereas microbial PstS have a well‐defined role in phosphate ABC transporters, the physiological function of DING proteins, named after their DINGGG N termini, still needs to be determined. PstS and DING proteins co‐exist in some Pseudomonas strains, to which they confer a highly adhesive and virulent phenotype. More than 30 DING proteins have now been purified, mostly from eukaryotes. They are often associated with infections or with dysregulation of cell proliferation. Consequently, eukaryotic DING proteins could also be involved in cell–cell communication or adherence. The ubiquitous presence in eukaryotes of proteins structurally and functionally related to bacterial virulence factors is intriguing, as is the absence of eukaryotic genes encoding DING proteins in databases. DING proteins in eukaryotes could originate from unidentified commensal or symbiotic bacteria and could contribute to essential functions. Alternatively, DING proteins could be encoded by eukaryotic genes sharing special features that prevent their cloning. Both hypotheses are discussed.     

Membrane proteins: shaping up

Over recent years, much progress has been made in the identification and characterization of factors involved in the biosynthesis of integral membrane proteins of the helix-bundle type. In addition, our knowledge of membrane protein structure and the forces stabilizing helix-helix interactions in a lipid environment is expanding rapidly. However, it is still not clear how a membrane protein folds into its final form in vivo, nor what constraints there are on the folded structure that results from the mechanistic details of translocon-mediated assembly rather than simply from the thermodynamics of protein-lipid interactions.     

Ribosome-inactivating proteins up to date

Ribosome-inactivating proteins (RIPs) from plants inactivate eukaryotic ribosomes, as far as studied by rendering their 60 S subunit unable to bind elongation factor 2. These proteins seem widely distributed and possibly ubiquitous in plants. They are either type 1, those consisting of a single polypeptide chain, or type 2 (ricin and related toxins), those consisting of two chains, one of which is a galactose-binding lectin. The literature on RIPs from 1982 has been reviewed with respect to the chemical and biological properties of RIPs, their use for the preparation of immunotoxins and new perspectives.     

DING proteins; novel members of a prokaryotic phosphate-binding protein superfamily which extends into the eukaryotic kingdom

PstS proteins are the cell-bound phosphate-binding elements of the ubiquitous bacterial ABC phosphate uptake mechanisms. Primary and tertiary structures, characteristic of pstS proteins, are conserved in proteins, which are expressed in secretory operons and induced by phosphate deprivation, in Pseudomonas species. There are two subsets of these proteins; AP proteins, which are alkaline phosphatases, and DING proteins, named for their N-terminal sequence, which are phosphate-binding proteins. Both form elements of a proposed phosphate-scavenging system in pseudomonads. DING proteins have also been isolated from many eukaryotic sources, and are associated with both normal and pathological functions in mammals. Their phosphate-binding function suggests a role in biomineralization, but the ability to bind other ligands may be related to signal transduction in eukaryotes. Though it has been claimed that all such proteins may originate from pseudomonads, many eukaryotic DING proteins have unique features which are incompatible with a bacterial origin.     

San1p, checking up on nuclear proteins

Cellular quality control mechanisms perform vital tasks by ensuring that the proteome reflects precisely the information encoded by the genome. In this issue of Cell, Gardner et al. (2005) report the discovery of a novel protein quality control system that resides in the nucleus. Central to this system is the E3 ligase San1p, which monitors nuclear proteins and targets aberrant species for destruction.     

Comparison of the DING protein from the archaeon Sulfolobus solfataricus with human phosphate-binding protein and Pseudomonas fluorescence DING counterparts

DING proteins represent a new group of 40 kDa-related members, ubiquitous in living organisms. The family also include the DING protein from Sulfolobus solfataricus, functionally related to poly(ADP-ribose) polymerases. Here, the archaeal protein has been compared with the human Phosphate-Binding Protein and the Pseudomonas fluorescence DING enzyme, by enzyme assays and immune cross-reactivity. Surprisingly, as the Sulfolobus enzyme, the Human and Pseudomonas proteins display poly(ADP-ribose) polymerase activity, whereas a phosphatase activity was only present in Sulfolobus and human protein, despite the conserved phosphate-binding site residues in Pseudomonas DING. All proteins were positive to anti-DING antibodies and gave a comparable pattern of anti-poly(ADP-ribose) polymerase immunoreactivity with two bands, at around 40 kDa and roughly at the double of this molecular mass. The latter signal was present in all Sulfolobus enzyme preparations and proved not due to either a contaminant or a precursor protein, but likely being a dimeric form of the 40 kDa polypeptide. The common immunological and partly enzymatic behavior linking human, Pseudomonas and Sulfolobus DING proteins, makes the archaeal protein an important model system to investigate DING protein function and evolution within the cell.

     

Lighting up cells: labelling proteins with fluorophores

During the past decade, rapid improvements have been made in the tools available for labelling proteins within cells, which has increased our ability to unravel the finer details of cellular events. One significant reason for these advances has been the development of fluorescent proteins that can be incorporated into proteins by genetic fusion to produce a fluorescent label. In addition, new techniques have made it possible to label proteins with small organic fluorophores and semiconductor nanocrystals.     

Receptor activity-modifying proteins: RAMPing up adrenomedullin signaling

Adrenomedullin (AM) is a 52-amino-acid multifunctional peptide that circulates in the plasma in the low picomolar range and can exert a multitude of biological effects through an autocrine/paracrine mode of action. The mechanism by which AM transduces its signal represents a novel and pharmacologically tractable paradigm in G protein-coupled receptor signaling. Since its discovery in 1993, the study of AM has emerged into a new field of research with nearly 1800 publications that rivals the renown of other common factors like angiopoetin (1015 publications) and ghrelin (1550 publications). Despite the tremendous strides made in recent years toward unveiling the biochemical and cellular functions of AM, we are still lagging in our understanding of the essential roles of AM in normal and disease physiology. As discussed in this current review, a concerted effort to combine information from clinical, genomic, biochemical, and genetic mouse model sources can provide a focused view to help define the physiological functions of AM. Specifically, we find that certain conditions, such as pregnancy, cardiovascular disease, and sepsis, are associated with robust and dynamic changes in the expression of AM and AM receptor proteins, which together represent an elegant mechanism for altering the physiological responsiveness or function of AM. Thus, the modulation of AM signaling may be further exploited for therapeutic strategies in the management and treatment of human disease.     

The SsgA-like proteins in actinomycetes: small proteins up to a big task

Several unique protein families have been identified that play a role in the control of developmental cell division in streptomycetes. The SsgA-like proteins or SALPs, of which streptomycetes typically have at least five paralogues, control specific steps of sporulation-specific cell division in streptomycetes, affecting cell wall-related events such as septum localization and synthesis, thickening of the spore wall and autolytic spore separation. The expression level of SsgA, the best studied SALP, has a rather dramatic effect on septation and on hyphal morphology, which is not only of relevance for our understanding of (developmental) cell division but has also been successfully applied in industrial fermentation, to improve growth and production of filamentous actinomycetes. Recent observations suggest that SsgB most likely is the archetypal SALP, with only SsgB orthologues occurring in all morphologically complex actinomycetes. Here we review 10 years of research on the SsgA-like proteins in actinomycetes and discuss the most interesting regulatory, functional, phylogenetic and applied aspects of this relatively unknown protein family.     

Ring and zipper formation is the key to understanding the structural variety in all-beta proteins

A novel structural classification of beta proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on the fact that 92% and 60% of beta proteins have the ring topology and the zippered contact pattern, respectively. We discuss the implication of the unexpectedly high preference for the ring and zippered structures in connection with the folding process of beta proteins.     

Membrane proteins shape up: understanding in vitro folding

Progress in structural biology has begun to reveal the precise architecture of integral membrane proteins. However, the manner in which these complex structures are achieved remains unclear. Recent developments are starting to shed light on the unfolding and folding of a small but growing number of membrane proteins. Mechanistic details derived from kinetic and thermodynamic experiments now enable comparison of the folding of different membrane proteins and their water-soluble cousins. This work also has important implications for other structural and functional studies of membrane proteins in vitro.