Proteome-derived Peptide Libraries Allow Detailed Analysis of the Substrate Specificities of Nα-acetyltransferases and Point to hNaa10p as the Post-translational Actin Nα-acetyltransferase

The impact of N^α-terminal acetylation on protein stability and protein function in general recently acquired renewed and increasing attention. Although the substrate specificity profile of the conserved enzymes responsible for N^α-terminal acetylation in yeast has been well documented, the lack of higher eukaryotic models has hampered the specificity profile determination of N^α-acetyltransferases (NATs) of higher eukaryotes. The fact that several types of protein N termini are acetylated by so far unknown NATs stresses the importance of developing tools for analyzing NAT specificities. Here, we report on a method that implies the use of natural, proteome-derived modified peptide libraries, which, when used in combination with two strong cation exchange separation steps, allows for the delineation of the in vitro specificity profiles of NATs. The human NatA complex, composed of the auxiliary hNaa15p (NATH/hNat1) subunit and the catalytic hNaa10p (hArd1) and hNaa50p (hNat5) subunits, cotranslationally acetylates protein N termini initiating with Ser, Ala, Thr, Val, and Gly following the removal of the initial Met. In our studies, purified hNaa50p preferred Met-Xaa starting N termini (Xaa mainly being a hydrophobic amino acid) in agreement with previous data. Surprisingly, purified hNaa10p preferred acidic N termini, representing a group of in vivo acetylated proteins for which there are currently no NAT(s) identified. The most prominent representatives of the group of acidic N termini are γ- and β-actin. Indeed, by using an independent quantitative assay, hNaa10p strongly acetylated peptides representing the N termini of both γ- and β-actin, and only to a lesser extent, its previously characterized substrate motifs. The immunoprecipitated NatA complex also acetylated the actin N termini efficiently, though displaying a strong shift in specificity toward its known Ser-starting type of substrates. Thus, complex formation of NatA might alter the substrate specificity profile as compared with its isolated catalytic subunits, and, furthermore, NatA or hNaa10p may function as a post-translational actin N^α-acetyltransferase.The multisubunit and ribosome-associated protein N^α-acetyltransferases (NATs)1 are omnipresent enzyme complexes that catalyze the transfer of the acetyl moiety from acetyl-CoA to the primary α-amines of N termini of nascent proteins (1–3). As up to 50 to 60% of yeast proteins and 80 to 90% of human proteins are modified in this manner, N^α-acetylation is a widespread protein modification in eukaryotes (4–7), and the pattern of modification has remained largely conserved throughout evolution (4, 8). NATs belong to a subfamily of the Gcn5-related N-acetyltransferase superfamily of N-acetyltransferases, additionally encompassing the well-studied histone acetyltransferases that are implicated in epigenetic imprinting.In yeast and humans, three main NAT complexes, NatA, NatB, and NatC were found to be responsible for the majority of N^α-terminal acetylations (1). The NatA complex, responsible for cotranslational N^α-terminal acetylation of proteins with Ser, Ala, Thr, Gly, and Val N termini, is composed of two main subunits, the catalytic subunit Naa10p (previously known as Ard1p) and the auxiliary subunit Naa15p (previously known as Nat1p/NATH) (9–11). Furthermore, a third catalytic subunit Naa50p (previously known as Nat5)—an acetyltransferase shown to function in chromosome cohesion and segregation (12–14)—was found to physically interact with the NatA complex of yeast (2), fruit fly (12), and human (15). Recently, human Naa50p (hNaa50p) was reported to display lysine or N^ε-acetyltransferase as well as NAT activity (16), the latter was defined as NatE activity (16). Interestingly, the chaperone-like, Huntingtin interacting protein HYPK, identified as a novel stable interactor of human NatA, was functionally implicated in the N-terminal acetylation of an in vivo NatA substrate, demonstrating that NAT complex formation and composition may have an overall influence on the observed (degree of) N^α-acetylation (17). Further, subunits of the human NatA complex have been coupled to cancer-related processes and differentiation, with altered subunit expression reported in papillary thyroid carcinoma, neuroblastoma, and retinoic acid induced differentiation. Furthermore, the NatA catalytic subunit was found to be implicated in processes such as hypoxia-response and the β-catenin pathway (18, 19). Of note is that in line with the differential localization patterns of the individual NatA subunits (9, 13, 20, 21), other data indicate that these subunits might well exert NatA-independent enzymatic functions (13, 22, 23). Given that a significant fraction of hNaa10p and hNaa15p are nonribosomal (9), and given the multitude of postulated post-translational in vivo N-acetylation events recently reported (24–26), these observations argue in favor of the existence of NAT complexes and/or catalytic NAT-subunits acting post-translationally.Similar to NatA, the NatB and NatC complexes, composed of the catalytic subunit Naa20p or Naa30p and the auxiliary subunits Naa25p or Naa35p and Naa38p respectively, are conserved from yeast to higher eukaryotes concerning their subunit composition as well as their substrate specificity. Both these complexes display activity toward methionine-starting N termini, with NatB preferring acidic residues as well as Asn and Gln at P2′-sites², whereas NatC prefers hydrophobic amino acid residues at substrate P2′-sites (1, 27, 28).N^α-acetylation affects various protein functions such as localization, activity, association, and stability (29, 30). Only recently a more generalized function of protein N^α-acetylation in generating so-called N-terminal degrons marking proteins for removal was put forward (31). The lack of mouse models in addition to the fact that (combined) knockdown of individual components of N^α-acetyltransferases only marginally affect the overall N^α-acetylation status (4) have so far hampered the molecular characterization of the substrate specificity profile of (yet uncharacterized) NATs. To date, all eukaryote N^α-acetylation events are assumed to be catalyzed by the five known NATs (32). However, an additional level of complexity is imposed by the fact that in contrast to yeast, higher eukaryotes express multiple splice variants of various NAT subunits as well as paralogs thereof (33, 34), further implicating that a specific NAT''s substrate specificity might be altered in this way, in addition to the possible existence of substrate redundancy. Moreover, regulation of substrate specificity and stability of NAT activity can be imposed by differential complex formation and post-translational modifications including phosphorylation, auto-acetylation, and specific proteolytic cleavage of the catalytic subunits (9, 16, 17). As such, a detailed understanding of the substrate specificity of NATs, and the regulation thereof, could help unravel the physiological substrate repertoires as well as the associated physiological roles of NATs in the normal and the disease state.The specificity of N^α-acetyltransferases and their endogenous substrates were originally studied by two-dimensional-PAGE: N^α-acetylation neutralizes the N-terminal positive charge, resulting in an altered electrophoretic protein migration during isoelectric focusing (35–38). Recently, this altered biophysical property was also exploited to enrich for protein N-termini using low pH strong cation exchange (SCX) chromatography (24, 39). As an example, SCX prefractionation combined with N-terminal combined fractional diagonal chromatography, a targeted proteomics technology negatively selecting for protein N-terminal peptides, stable isotope labeling of amino acids in cell culture, and amino-directed modifiers (40), was used to study the in vivo substrate repertoires of human as well as yeast NatA (4).Nevertheless, the various methods reported today to study in detail N^α-terminal acetylation and thus the specificities of different NATs make use of a limited and therefore somewhat biased set of synthesized peptide substrates and comprise the rather laborious detection of radioactive acetylated products as well as enzyme-coupled methods quantifying acetyl-CoA conversion. Because (proteome-derived) peptide libraries have been used extensively to study epitope mapping (41), protein-protein interactions (42), protein modifications such as phosphorylation (43), and proteolysis (44, 45), as well as for determining the substrate specificity of the N^α-deblocking peptide deformylase (46), we reckoned that the development of an oligopeptide-based acetylation assay should allow for more comprehensive screening of NAT-like activities. We here report on the development of a peptide-based method to systematically screen for the in vitro sequence specificity profile of individual NATs as well as endogenous NAT complexes. In summary, SCX enriched, N^α-free peptide libraries, derived from natural proteomes build up the peptide substrate pool. And, upon incubation, NAT N^α-acetylated peptides are enriched by a second SCX fractionation step, resulting in a positive selection of NAT-specific peptide substrates. By use of this proteome-derived peptide library approach, we here delineated (differences in) the specificity profiles of hNaa50p and hNaa10p as isolated hNatA components, as well as of assayed their combined activity when in their native hNatA complex.     

Degradation of extracellular matrix by mouse trophoblast outgrowths: a model for implantation

During implantation the embryo attaches to the endometrial surface and trophoblast traverses the uterine epithelium, anchoring in the uterine connective tissue. To determine whether trophoblast can facilitate invasion of the uterus by degrading components of normal uterine extracellular matrix, mouse blastocysts were cultured on a radio-labeled extracellular matrix that contained glycoproteins, elastin, and collagen. The embryos attached to the matrix, and trophoblast spread over the surface. Starting on day 5 of culture there was a release of labeled peptides into the medium. The radioactive peptides released from the matrix by the embryos had molecular weights ranging from more than 25,000 to more than 200. By day 7 there were areas where individual trophoblast cells had separated from one another, revealing the underlying substratum that was cleared of matrix. When trophoblast cells were lysed with NH(4)OH on day 8, it was apparent that the area underneath the trophoblast outgrowth had been cleared of matrix. Scanning electron microscopy and time-lapse cinemicrography confirmed that the digestion of matrix was highly localized, taking place only underneath the trophoblast, with no evidence of digestion of the matrix beyond the periphery of the trophoblast outgrowth. The sharp boundaries of degredation observed may be due to localized proteinase secretion by trophoblast, to membrane proteinases on the surface of trophoblast, or to endocytosis. Digestion of the matrix was not dependent on plasminogen, thus ruling out a role for plasminogen activator. Digestion was not inhibited by a variety of hormones and inhibitors, including progesterone, 17β-estradiol, leupeptin, EDTA, colchicine, NH(4)Cl, or ε-aminocaproic acid. This system of culturing embryos on extracellular matrix may be useful in determining the processes that regulate trophoblast migration and invasion into the maternal tissues during implantation.0     

Glucose-stimulated insulin response in pregnant sheep following acute suppression of plasma non-esterified fatty acid concentrations

Background  

Elevated non-esterified fatty acids (NEFA) concentrations in non-pregnant animals have been reported to decrease pancreatic responsiveness. As ovine gestation advances, maternal insulin concentrations fall and NEFA concentrations increase. Experiments were designed to examine if the pregnancy-associated rise in NEFA concentration is associated with a reduced pancreatic sensitivity to glucose in vivo. We investigated the possible relationship of NEFA concentrations in regulating maternal insulin concentrations during ovine pregnancy at three physiological states, non-pregnant, non-lactating (NPNL), 105 and 135 days gestational age (dGA, term 147+/- 3 days).     

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

Nitrous oxide (N₂O) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to nitrogen gas (N₂) by bacteria and archaea harboring the N₂O reductase (N₂OR), which is the only known N₂O sink in the biosphere. Despite its crucial role in mitigating N₂O emissions, knowledge of the N₂OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N₂OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N₂O-reducing communities. Examination of N₂OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N₂OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various environments showed that it is widespread and diverse. Using quantitative PCR, we demonstrate that this clade was most often at least as abundant as the other, thereby more than doubling the known extent of the overall N₂O-reducing community in the environment. Furthermore, we observed that the relative abundance of nosZ from either clade varied among habitat types and environmental conditions. Our results indicate a physiological dichotomy in the diversity of N₂O-reducing microorganisms, which might be of importance for understanding the relationship between the diversity of N₂O-reducing microorganisms and N₂O reduction in different ecosystems.