Production of Extracellular Polysaccharides by CAP Mutants of Cryptococcus neoformans

The human pathogen Cryptococcus neoformans causes meningoencephalitis. The polysaccharide capsule is one of the main virulence factors and consists of two distinct polysaccharides, glucuronoxylomannan (GXM) and galactoxylomannan (GalXM). How capsular polysaccharides are synthesized, transported, and assembled is largely unknown. Previously, it was shown that mutations in the CAP10, CAP59, CAP60, and CAP64 genes result in an acapsular phenotype. Here, it is shown that these acapsular mutants do secrete GalXM and GXM-like polymers. GXM and GalXM antibodies specifically reacted with whole cells and the growth medium of the wild type and CAP mutants, indicating that the capsule polysaccharides adhere to the cell wall and are shed into the environment. These polysaccharides were purified from the medium, either with or without anion-exchange chromatography. Monosaccharide analysis of polysaccharide fractions by gas-liquid chromatography/mass spectrometry showed that wild-type cells secrete both GalXM and GXM. The CAP mutants, on the other hand, were shown to secrete GalXM and GXM-like polymers. Notably, the GalXM polymers were shown to contain glucuronic acid. One-dimensional ¹H nuclear magnetic resonance confirmed that the CAP mutants secrete GalXM and also showed the presence of O-acetylated polymers. This is the first time it is shown that CAP mutants secrete GXM-like polymers in addition to GalXM. The small amount of this GXM-like polymer, 1 to 5% of the total amount of secreted polysaccharides, may explain the acapsular phenotype.Cryptococcus neoformans of the A (var. grubii [24]) and D (var. neoformans [36]) serotypes are the causative agents of cryptococcosis, of which the most common clinical form is meningoencephalitis. This disease is related to immunocompromised patients but can also occur in immunocompetent individuals (4, 19, 38). One of the main virulence factors is the polysaccharide capsule (2, 5, 17, 21, 27, 35). This capsule enables the yeast-like fungus to survive the harsh environment of the human body by using its immunomodulatory properties that enable immune evasion and by preventing killing through phagocytosis by macrophages (44, 45).The capsule consists of a low percentage of mannoproteins (46) and the polysaccharides glucuronoxylomannan (GXM) and galactoxylomannan (GalXM) in a mass ratio of about 10:1 (14, 16, 17). Little is known about the synthesis of GXM and GalXM and their transport toward the cell surface. A mutation in the Sec4/Rab8 GTPase homologue was recently shown to affect protein secretion as well as polysaccharide secretion and resulted in intracellular accumulation of vesicles containing GXM (51). From this and the fact that GXM has been detected in extracellular vesicles, it was proposed that polysaccharides are packaged in such vesicles to cross the cell wall to reach the extracellular environment (47).Mutation analysis has revealed four genes, called CAP10, CAP59, CAP60, and CAP64, which give an acapsular phenotype when inactivated (7, 9-13). The precise role of the encoded Cap proteins is unknown. Cap59 has been suggested to play a role in extracellular trafficking of multimeric forms of GXM molecules (26). Moreover, it may play a role in the assembly of GXM, since it shares homology with a mannosyltransferase (48). Like Cap59, Cap60 is a putative mannosyltransferase. Cap10 shares homology with a xylosyltransferase and therefore may also be involved in capsule assembly (34), like the recently identified xylosyltransferase encoded by CXT1 (33). This transferase has been shown to play a direct role in the synthesis of both of the capsular polysaccharides but is especially active in the addition of xyloses to the GalXM polysaccharide. CAP64 shares homology with so-called CAS genes, encoding proteins involved in O acetylation of GXM (40).Structural analysis has revealed a relatively clear picture of the buildup of the GXM and GalXM polysaccharides (14, 50) (Fig. ​(Fig.1).1). Some variability in the chemical structures of the capsular polysaccharides has been described, even within the capsule of a particular strain (40, 50). In addition, GalXM has been shown to also contain, besides galactopyranose, galactofuranose in trace amounts (1, 29). The two C. neoformans serotypes A and D are distinguished based on variation in the position of the different xylose residues in the GXM repeating unit (30). The structure of the GalXM repeating unit was analyzed by using a fraction of purified polysaccharides secreted in the medium by a mutant of the D serotype called the CAP67 mutant. This strain is mutated in the same gene as a serotype A CAP59 mutant. The number of xylose residues can vary from zero up to six within the GalXM repeating unit (Fig. ​(Fig.1)1) (50).Open in a separate windowFIG. 1.Chemical structure of GXM and GalXM monomers. Large strands of these monomers form polymers of up to 1 × 10⁶ to 7 × 10⁶ daltons for GXM and 1 × 10⁵ daltons for GalXM. Ratios vary between serotypes. Shown are serotype A GXM, Man 3/Xyl 2/GlcA 1, and GalXM, Gal 6/Man 4/Xyl 1.6 (shown are three xyloses). The degree of O acetylation is not shown. The picture is based on data from reference 3.So far, secreted polysaccharides in the medium of the serotype D CAP67 mutant and the corresponding serotype A CAP59 mutant have been analyzed (41, 50). It was shown that these mutants secrete GalXM but not GXM in the medium. However, it is shown here that these mutants, as well as the serotype A CAP10, CAP60, and CAP64 mutants, also secrete GXM-like polymers in addition to GalXM. Moreover, part of GalXM seems to contain glucuronic acid, supporting earlier findings (16, 49).     

Isocitrate Dehydrogenase Is Important for Nitrosative Stress Resistance in Cryptococcus neoformans,but Oxidative Stress Resistance Is Not Dependent on Glucose-6-Phosphate Dehydrogenase

The opportunistic intracellular fungal pathogen Cryptococcus neoformans depends on many antioxidant and denitrosylating proteins and pathways for virulence in the immunocompromised host. These include the glutathione and thioredoxin pathways, thiol peroxidase, cytochrome c peroxidase, and flavohemoglobin denitrosylase. All of these ultimately depend on NADPH for either catalytic activity or maintenance of a reduced, functional form. The need for NADPH during oxidative stress is well established in many systems, but a role in resistance to nitrosative stress has not been as well characterized. In this study we investigated the roles of two sources of NADPH, glucose-6-phosphate dehydrogenase (Zwf1) and NADP⁺-dependent isocitrate dehydrogenase (Idp1), in production of NADPH and resistance to oxidative and nitrosative stress. Deletion of ZWF1 in C. neoformans did not result in an oxidative stress sensitivity phenotype or changes in the amount of NADPH produced during oxidative stress compared to those for the wild type. Deletion of IDP1 resulted in greater sensitivity to nitrosative stress than to oxidative stress. The amount of NADPH increased 2-fold over that in the wild type during nitrosative stress, and yet the idp1Δ strain accumulated more mitochondrial damage than the wild type during nitrosative stress. This is the first report of the importance of Idp1 and NADPH for nitrosative stress resistance.The alveolar macrophage can produce microbicidal amounts of toxic reactive oxygen species (ROS) and reactive nitrogen species (RNS) following phagocytosis (27, 53). Despite this, the opportunistic fungal pathogen Cryptococcus neoformans is able to inhabit and replicate within phagocytes of the mammalian host and to exit these cells unharmed (1, 2, 40). The intracellular pathogenicity of C. neoformans is most likely facilitated by stress resistance mechanisms, including a number of antioxidant proteins and pathways involved in the detoxification of ROS and RNS. Specifically, these include the synthesis of mannitol, a free radical scavenger (9, 20); the small protein flavohemoglobin denitrosylase (Fhb1), which is essential for resistance of C. neoformans to nitrosative stress (10, 14, 32); and the glutathione and thioredoxin antioxidant systems, which are both important for stress resistance and virulence (42, 43, 45).Even with different mechanisms of catalysis and/or cellular localization, one thing that these stress resistance proteins and pathways have in common is the requirement for NADPH as a cofactor. NADPH is used as an electron donor either in recycling of oxidized, inactive enzymes to reduced, active forms or directly in catalytic activity. For example, Fhb1 binds NADPH during its catalytic activity and uses it directly as an electron donor for the reduction of NO· to NO₃ (21). Catalases, which are highly conserved antioxidants that dismute H₂O₂ to molecular oxygen and water, consist of four units each with a molecule of NADPH bound in the core (18, 36, 59). The tripeptide glutathione (GSH) is oxidized to glutathione disulfide (GSSG), a homodimer held together by a disulfide bridge, during its oxidative state. GSSG can be reduced back to GSH by glutathione reductase, an enzyme that requires NADPH for electrons used in reduction. Similarly, glutathione peroxidase and thiol peroxidase ultimately depend on NADPH for recycling from an oxidized, inactive form back to a reduced, active form (57).NADPH is classically recognized as being produced by the highly conserved, cytosolic pentose phosphate pathway. This pathway has been shown to be important for reductive biochemistry during oxidative stress in many organisms. The pentose phosphate pathway is an essential factor in maintaining health of erythrocytes, cells that, due to their biological function, have considerable risk for oxidative damage. Humans deficient in the pathway have hemolytic anemia, as their erythrocytes are unable to maintain sufficient pools of reduced glutathione (68). Also, the pressure of oxidative stress can stimulate the pentose phosphate pathway. This has been shown in human lymphocytes (56); in the rat adrenal gland, liver, and pancreas (15, 16); and in bacteria (63).In fungi, the pentose phosphate pathway has been implicated in both oxidative stress resistance and adaptation to oxidative stress. In the model yeast Saccharomyces cerevisiae, NADPH-generating systems, including the pentose phosphate pathway, are critical for the ability of this organism to resist and adapt to high levels of oxidative stress (35, 47). It has also been shown that the cytosolic copper/zinc superoxide dismutase and the pentose phosphate pathway have overlapping roles in protecting S. cerevisiae from oxidative stress and that both systems are critical for maintaining the intracellular redox state (62). Furthermore, fungi may rely on the pentose phosphate pathway for more than reducing oxidative stress. Aspergillus nidulans requires a functional pentose phosphate pathway for nitrogen metabolism. Four A. nidulans mutants with independent defects in the pentose phosphate pathway were unable to grow on nitrite, nitrate, or various carbon sources, including 1% glucose, d-xylose, or d-glucoronate (28).The pathway has two phases, the oxidative phase and the nonoxidative phase. The oxidative phase consists of two successive oxidations and results in the production of NADPH. The first enzyme in the oxidative phase of the pentose phosphate pathway is glucose-6-phosphate dehydrogenase (Zwf). Zwf catalyzes the oxidation of glucose-6-phosphate to 6-phosphogluconate and is highly specific for NADP⁺ as a cofactor (49, 67). There is abundant evidence supporting the role of Zwf in oxidative stress resistance. In addition to Zwf deficiency causing hemolytic anemia, Zwf has been also been implicated in maintenance of DNA repair systems during oxidative stress, as some cancers and aging disorders have also been linked to Zwf deficiency (30). For instance, Chinese hamster ovarian cells that are Zwf null have enhanced radiation sensitivity and a reduced ability to repair double-strand breaks due to the inactivation of Ku, a heterodimer DNA repair protein. In this case, the inactivation of Ku is the result of overoxidation of key cysteine residues on the protein due to the lack of sufficient reduced GSH (3). In the model yeast Saccharomyces cerevisiae, deletion of ZWF1 results in sensitivity to oxidative stress. ZWF1 is also important for the adaptive response to oxidative stress in S. cerevisiae. ZWF1-null mutants and wild-type cells were pretreated with 0.2 mM H₂O₂ and then challenged with 2 mM H₂O₂. While a large increase in tolerance to the high level of H₂O₂ was observed in the wild-type cells pretreated with 0.2 mM H₂O₂, the zwf1Δ strain was unable to tolerate the higher concentration (33). In Candida albicans, another pathogenic fungus, ZWF1 is upregulated during oxidative stress (38).Another source of NADPH is NADP⁺-dependent isocitrate dehydrogenase (Idp) (55), a ubiquitous enzyme that in systems ranging from humans to yeasts to plants has been found in the cytosol, peroxisomes, or mitochondria (12, 19, 70). Although this enzyme can be targeted to mitochondria, it is distinct from the NAD⁺-dependent isocitrate dehydrogenase (Idh) that functions in the mitochondria as part of the Krebs cycle. However, similarly to Idh, Idp catalyzes the decarboxylation of isocitrate to α-ketoglutarate (29). This reaction can be performed in the mitochondria, in the cytosol, or in peroxisomes using isocitrate formed from citrate exported across the mitochondrial membrane. This allows for the production of NADPH in cellular compartments without reliance of active transport of NADPH across membranes (11). It is important to have reductive power produced directly within organelles for protection from exogenous as well as endogenous stressor. For example, NADPH is consumed in peroxisomes by enzymes such as catalase and uric acid oxidase, that counteract the ROS produced during breakdown of lipids (4, 5, 31). Mitochondria particularly require reductive capability, as these organelles are susceptible to endogenous ROS produced during cellular respiration and also to exogenous RNS (52). The proteins that make up the electron transport chain are prone to damage by nitric oxide, peroxynitrite, and S-nitrosothiols (6). Nitric oxide and peroxynitrite have been shown to cause irreversible damage to cytochrome c reductase, NADH dehydrogenase, and the succinate-ubiquinone complex; the common mechanism of damage is sequestration of iron/sulfur centers of the proteins (54, 69). Thus, without a means of detoxification, the mitochondrial membrane loses potential and the ability to continue respiration, leading to death of the stressed cell. In C. neoformans, some antioxidant enzymes that are located at the mitochondria and dependent on NADPH for function include catalases, superoxide dismutases, cytochrome c peroxidase, and flavohemoglobin denitrosylase (7, 24, 25, 26). These enzymes are important for stress resistance or virulence of C. neoformans due to their role in high-temperature growth (24, 25) or nitrosative stress resistance (10, 14, 26).In humans, there is one IDP gene that results in mitochondrial and peroxisomal products (22). In S. cerevisiae, there are three IDP genes, which encode mitochondrial (IDP1), cytosolic (IDP2), and peroxisomal (IDP3) forms of the protein. Deletion of both ZWF1 and any one of the IDP genes in S. cerevisiae results in sensitivity to oxidative stress, likely due to a substantial decrease in NADPH produced in these double deletion mutants (41). In C. neoformans there is one predicted IDP gene (IDP1). Microarray data have indicated that this gene is upregulated 2.5-fold during nitrosative stress and thus may have a role in resistance to this stressor (44).Since so many factors essential for stress resistance in C. neoformans utilize NADPH, we hypothesize that the sources of this cofactor are likewise critical for stress resistance. Although Zwf1 is important for adaptation to oxidative stress in the fungi S. cerevisiae and C. albicans, we had previously found that C. neoformans is unable to adapt to oxidative stress (S. M. Brown and J. K. Lodge, unpublished data), and thus we had reason to suspect that the role of Zwf1 in C. neoformans may be different than that in other organisms. The role of Idp1 in stress resistance, especially in resistance to nitrosative stress, is relatively unknown. In this study we used biochemical and genetic approaches to compare the roles of Zwf1 and Idp1 in resistance to oxidative and nitrosative stress in C. neoformans. We found that the Zwf1 is dispensable for viability, for resistance to oxidative and nitrosative stress, and for NADPH production. In contrast, we found that Idp1 is important for resistance to nitrosative stress, specifically for maintaining healthy mitochondria during exposure to nitrosative stress.     

Melanin Externalization in Candida albicans Depends on Cell Wall Chitin Structures

The fungal pathogen Candida albicans produces dark-pigmented melanin after 3 to 4 days of incubation in medium containing l-3,4-dihydroxyphenylalanine (l-DOPA) as a substrate. Expression profiling of C. albicans revealed very few genes significantly up- or downregulated by growth in l-DOPA. We were unable to determine a possible role for melanin in the virulence of C. albicans. However, we showed that melanin was externalized from the fungal cells in the form of electron-dense melanosomes that were free or often loosely bound to the cell wall exterior. Melanin production was boosted by the addition of N-acetylglucosamine to the medium, indicating a possible association between melanin production and chitin synthesis. Melanin externalization was blocked in a mutant specifically disrupted in the chitin synthase-encoding gene CHS2. Melanosomes remained within the outermost cell wall layers in chs3Δ and chs2Δ chs3Δ mutants but were fully externalized in chs8Δ and chs2Δ chs8Δ mutants. All the CHS mutants synthesized dark pigment at equivalent rates from mixed membrane fractions in vitro, suggesting it was the form of chitin structure produced by the enzymes, not the enzymes themselves, that was involved in the melanin externalization process. Mutants with single and double disruptions of the chitinase genes CHT2 and CHT3 and the chitin pathway regulator ECM33 also showed impaired melanin externalization. We hypothesize that the chitin product of Chs3 forms a scaffold essential for normal externalization of melanosomes, while the Chs8 chitin product, probably produced in cell walls in greater quantity in the absence of CHS2, impedes externalization.Candida albicans is a major opportunistic fungal human pathogen that causes a wide variety of infections (9, 68). In healthy individuals C. albicans resides as a commensal within the oral cavity and gastrointestinal and urogenital tracts. However, in immunocompromised hosts, C. albicans causes infections ranging in severity from mucocutaneous infections to life-threatening disseminated diseases (9, 68). Research into the pathogenicity of C. albicans has revealed a complex mix of putative virulence factors (7, 60), perhaps reflecting the fine balance this species strikes between commensal colonization and opportunistic invasion of the human host.Melanins are biological pigments, typically dark brown or black, formed by the oxidative polymerization of phenolic compounds. They are negatively charged hydrophobic molecules with high molecular weights and are insoluble in both aqueous and organic solvents. Their insolubility makes melanins difficult to study, and no definitive structure has yet been found for them; they probably represent an amorphous mixture of polymers (35). There are various types of melanin in nature, including eumelanin and phaeomelanin (76). Two principal types of melanin are found in the fungal kingdom. The majority are 1.8-dihydroxynapthalene (DNH) melanins synthesized from acetyl-coenzyme A (CoA) via the polyketide pathway (5). DNH melanins have been found in a wide range of opportunistic fungal pathogens of humans, including dark (dematiaceous) molds, such as Cladosporium, Fonsecaea, Phialophora, and Wangiella species, and as conidial pigments in Aspergillus fumigatus and Aspergillus niger (41, 80, 87, 88). However, several other fungal pathogens, including Blastomyces dermatitidis, Coccidioides posadasii, Cryptococcus neoformans, Histoplasma capsulatum, Paracoccidioides brasiliensis, and Sporothrix schenckii, produce eumelanin (3,4-dihydroxyphenylalanine [DOPA]-melanin) through the activity of a polyphenol oxidase (laccase) and require an exogenous o-diphenolic or p-diphenolic substrate, such as l-DOPA (16, 30, 63,–65, 67, 79).The production of melanin in humans and other mammals is a function of specialized cells called melanocytes. Particles of melanin polymers, sometimes, including more than one melanin type, are built up within membrane-bound organelles called melanosomes (76), and these are actively transported along microtubules to the tips of dendritic outgrowths of melanocytes, from where they are transferred to neighboring cells (32, 81). The mechanism of intercellular transfer of melanosomes has not yet been established, but the export process probably involves the fusion of cell and vesicular membranes rather than secretion of naked melanin (82). In pathogenic fungi, melanins are often reported to be associated with or “in” the cell wall (35, 36, 50, 72, 79). However, there is variation between species: the melanin may be located external to the wall, e.g., in P. brasiliensis (79); within the wall itself (reviewed in reference 42); or as a layer internal to the wall and external to the cell membrane, e.g., in C. neoformans (22, 45, 85). However, mutants of C. neoformans bearing disruptions of three CDA genes involved in the biosynthesis of cell wall chitosan, or of CHS3, encoding a chitin synthase, or of CSR2, which probably regulates Chs3, all released melanin into the culture supernatant, suggesting a role for chitin or chitosan in retaining the pigment polymer in its normal intracellular location (3, 4). However, vesicles externalized from C. neoformans cells also show laccase activity (21), so the effect of chitin may be on vesicle externalization rather than on melanin itself. Internal structures compatible with mammalian melanosomes have been observed in Cladosporium carrionii (73) and in Fonsecaea pedrosoi (2, 26). Remarkably, F. pedrosoi also secretes melanin and locates the polymer within the cell wall (1, 2, 25, 27, 74).Melanization has been found to play an important role in the virulence of several human fungal pathogens, such as C. neoformans, A. fumigatus, P. brasiliensis, S. schenckii, H. capsulatum, B. dermatitidis, and C. posadasii (among recent reviews are references 29, 42, 62, 74, and 79). From these and earlier reviews of the extensive literature, melanin has been postulated to be involved in a range of virulence-associated properties, including interactions with host cells; protection against oxidative stresses, UV light, and hydrolytic enzymes; resistance to antifungal agents; iron-binding activities; and even the harnessing of ionizing radiation in contaminated soils (15). The most extensively studied fungal pathogen for the role of melanization is C. neoformans, which possesses two genes, LAC1 and LAC2, encoding melanin-synthesizing laccases (52, 69, 90). It has been known since early studies with naturally occurring albino variants of C. neoformans (39) that melanin-deficient strains are attenuated in mouse models of cryptococcosis. Deletion of both the LAC1 and LAC2 genes reduced survival of C. neoformans in macrophages (52), and a study based on otherwise isogenic LAC1⁺ and LAC1⁻ strains confirmed the importance of LAC1 in experimental virulence (66). Other genes in the regulatory pathway for LAC1 are similarly known to be essential to virulence (12, 84).C. albicans has been shown to produce melanin with DOPA as a substrate for production of the polymer (53). The cells could be treated with hot acids to produce typical melanin “ghosts,” and antibodies specific for melanin reacted with the fungal cells by immunohistochemistry with tissues from experimentally infected mice, demonstrating that C. albicans produces melanin in vivo (53). However, no candidate genes encoding laccases have yet been identified in the C. albicans genome (http://www.candidagenome.org/). In this study, we investigated the production of melanin by C. albicans and showed that its normal externalization from wild-type cells, including formation of melanosomes, can be altered to an intracellular and intrawall location by mutation of genes involved in chitin synthesis. C. albicans has four genes encoding chitin synthase enzymes. CHS1 is an essential gene under normal conditions (59), and its product is the main enzyme involved in septum formation (83). Chs3 forms the bulk of the chitin in the cell wall and the chitinous ring at sites of bud emergence (8, 51, 57), while Chs2 contributes to differential chitin levels found between yeast and hyphal forms of the fungus, and Chs8 influences the architecture of chitin microfibrils (43, 51, 55, 57, 58). We found that melanin externalization was unaffected in a chs8Δ mutant but was reduced or abrogated in chs2Δ and chs3Δ mutants. Expression profiles of melanin-producing cells grown in the presence of l-DOPA did not identify any potential laccase-synthesizing genes.     

High-definition De Novo Sequencing of Crustacean Hyperglycemic Hormone (CHH)-family Neuropeptides

A complete understanding of the biological functions of large signaling peptides (>4 kDa) requires comprehensive characterization of their amino acid sequences and post-translational modifications, which presents significant analytical challenges. In the past decade, there has been great success with mass spectrometry-based de novo sequencing of small neuropeptides. However, these approaches are less applicable to larger neuropeptides because of the inefficient fragmentation of peptides larger than 4 kDa and their lower endogenous abundance. The conventional proteomics approach focuses on large-scale determination of protein identities via database searching, lacking the ability for in-depth elucidation of individual amino acid residues. Here, we present a multifaceted MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, a class of peptide hormones that play central roles in the regulation of many important physiological processes of crustaceans. Six crustacean CHH-family neuropeptides (8–9.5 kDa), including two novel peptides with extensive disulfide linkages and PTMs, were fully sequenced without reference to genomic databases. High-definition de novo sequencing was achieved by a combination of bottom-up, off-line top-down, and on-line top-down tandem MS methods. Statistical evaluation indicated that these methods provided complementary information for sequence interpretation and increased the local identification confidence of each amino acid. Further investigations by MALDI imaging MS mapped the spatial distribution and colocalization patterns of various CHH-family neuropeptides in the neuroendocrine organs, revealing that two CHH-subfamilies are involved in distinct signaling pathways.Neuropeptides and hormones comprise a diverse class of signaling molecules involved in numerous essential physiological processes, including analgesia, reward, food intake, learning and memory (1). Disorders of the neurosecretory and neuroendocrine systems influence many pathological processes. For example, obesity results from failure of energy homeostasis in association with endocrine alterations (2, 3). Previous work from our lab used crustaceans as model organisms found that multiple neuropeptides were implicated in control of food intake, including RFamides, tachykinin related peptides, RYamides, and pyrokinins (4–6).Crustacean hyperglycemic hormone (CHH)¹ family neuropeptides play a central role in energy homeostasis of crustaceans (7–17). Hyperglycemic response of the CHHs was first reported after injection of crude eyestalk extract in crustaceans. Based on their preprohormone organization, the CHH family can be grouped into two sub-families: subfamily-I containing CHH, and subfamily-II containing molt-inhibiting hormone (MIH) and mandibular organ-inhibiting hormone (MOIH). The preprohormones of the subfamily-I have a CHH precursor related peptide (CPRP) that is cleaved off during processing; and preprohormones of the subfamily-II lack the CPRP (9). Uncovering their physiological functions will provide new insights into neuroendocrine regulation of energy homeostasis.Characterization of CHH-family neuropeptides is challenging. They are comprised of more than 70 amino acids and often contain multiple post-translational modifications (PTMs) and complex disulfide bridge connections (7). In addition, physiological concentrations of these peptide hormones are typically below picomolar level, and most crustacean species do not have available genome and proteome databases to assist MS-based sequencing.MS-based neuropeptidomics provides a powerful tool for rapid discovery and analysis of a large number of endogenous peptides from the brain and the central nervous system. Our group and others have greatly expanded the peptidomes of many model organisms (3, 18–33). For example, we have discovered more than 200 neuropeptides with several neuropeptide families consisting of as many as 20–40 members in a simple crustacean model system (5, 6, 25–31, 34). However, a majority of these neuropeptides are small peptides with 5–15 amino acid residues long, leaving a gap of identifying larger signaling peptides from organisms without sequenced genome. The observed lack of larger size peptide hormones can be attributed to the lack of effective de novo sequencing strategies for neuropeptides larger than 4 kDa, which are inherently more difficult to fragment using conventional techniques (34–37). Although classical proteomics studies examine larger proteins, these tools are limited to identification based on database searching with one or more peptides matching without complete amino acid sequence coverage (36, 38).Large populations of neuropeptides from 4–10 kDa exist in the nervous systems of both vertebrates and invertebrates (9, 39, 40). Understanding their functional roles requires sufficient molecular knowledge and a unique analytical approach. Therefore, developing effective and reliable methods for de novo sequencing of large neuropeptides at the individual amino acid residue level is an urgent gap to fill in neurobiology. In this study, we present a multifaceted MS strategy aimed at high-definition de novo sequencing and comprehensive characterization of the CHH-family neuropeptides in crustacean central nervous system. The high-definition de novo sequencing was achieved by a combination of three methods: (1) enzymatic digestion and LC-tandem mass spectrometry (MS/MS) bottom-up analysis to generate detailed sequences of proteolytic peptides; (2) off-line LC fractionation and subsequent top-down MS/MS to obtain high-quality fragmentation maps of intact peptides; and (3) on-line LC coupled to top-down MS/MS to allow rapid sequence analysis of low abundance peptides. Combining the three methods overcomes the limitations of each, and thus offers complementary and high-confidence determination of amino acid residues. We report the complete sequence analysis of six CHH-family neuropeptides including the discovery of two novel peptides. With the accurate molecular information, MALDI imaging and ion mobility MS were conducted for the first time to explore their anatomical distribution and biochemical properties.     

A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells

Protein–protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, we have developed a new in vivo cross-linking mass spectrometry platform that couples a novel membrane-permeable, enrichable, and MS-cleavable cross-linker with multistage tandem mass spectrometry. This strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells and thus enables the determination of protein interaction interfaces. The utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and the targeted protein complex level. Our work represents a general approach for studying in vivo PPIs and provides a solid foundation for future studies toward the complete mapping of PPI networks in living systems.Protein–protein interactions (PPIs)¹ play a key role in defining protein functions in biological systems. Aberrant PPIs can have drastic effects on biochemical activities essential to cell homeostasis, growth, and proliferation, and thereby lead to various human diseases (1). Consequently, PPI interfaces have been recognized as a new paradigm for drug development. Therefore, mapping PPIs and their interaction interfaces in living cells is critical not only for a comprehensive understanding of protein function and regulation, but also for describing the molecular mechanisms underlying human pathologies and identifying potential targets for better therapeutics.Several strategies exist for identifying and mapping PPIs, including yeast two-hybrid, protein microarray, and affinity purification mass spectrometry (AP-MS) (2–5). Thanks to new developments in sample preparation strategies, mass spectrometry technologies, and bioinformatics tools, AP-MS has become a powerful and preferred method for studying PPIs at the systems level (6–9). Unlike other approaches, AP-MS experiments allow the capture of protein interactions directly from their natural cellular environment, thus better retaining native protein structures and biologically relevant interactions. In addition, a broader scope of PPI networks can be obtained with greater sensitivity, accuracy, versatility, and speed. Despite the success of this very promising technique, AP-MS experiments can lead to the loss of weak/transient interactions and/or the reorganization of protein interactions during biochemical manipulation under native purification conditions. To circumvent these problems, in vivo chemical cross-linking has been successfully employed to stabilize protein interactions in native cells or tissues prior to cell lysis (10–16). The resulting covalent bonds formed between interacting partners allow affinity purification under stringent and fully denaturing conditions, consequently reducing nonspecific background while preserving stable and weak/transient interactions (12–16). Subsequent mass spectrometric analysis can reveal not only the identities of interacting proteins, but also cross-linked amino acid residues. The latter provides direct molecular evidence describing the physical contacts between and within proteins (17). This information can be used for computational modeling to establish structural topologies of proteins and protein complexes (17–22), as well as for generating experimentally derived protein interaction network topology maps (23, 24). Thus, cross-linking mass spectrometry (XL-MS) strategies represent a powerful and emergent technology that possesses unparalleled capabilities for studying PPIs.Despite their great potential, current XL-MS studies that have aimed to identify cross-linked peptides have been mostly limited to in vitro cross-linking experiments, with few successfully identifying protein interaction interfaces in living cells (24, 25). This is largely because XL-MS studies remain challenging due to the inherent difficulty in the effective MS detection and accurate identification of cross-linked peptides, as well as in unambiguous assignment of cross-linked residues. In general, cross-linked products are heterogeneous and low in abundance relative to non-cross-linked products. In addition, their MS fragmentation is too complex to be interpreted using conventional database searching tools (17, 26). It is noted that almost all of the current in vivo PPI studies utilize formaldehyde cross-linking because of its membrane permeability and fast kinetics (10–16). However, in comparison to the most commonly used amine reactive NHS ester cross-linkers, identification of formaldehyde cross-linked peptides is even more challenging because of its promiscuous nonspecific reactivity and extremely short spacer length (27). Therefore, further developments in reagents and methods are urgently needed to enable simple MS detection and effective identification of in vivo cross-linked products, and thus allow the mapping of authentic protein contact sites as established in cells, especially for protein complexes.Various efforts have been made to address the limitations of XL-MS studies, resulting in new developments in bioinformatics tools for improved data interpretation (28–32) and new designs of cross-linking reagents for enhanced MS analysis of cross-linked peptides (24, 33–39). Among these approaches, the development of new cross-linking reagents holds great promise for mapping PPIs on the systems level. One class of cross-linking reagents containing an enrichment handle have been shown to allow selective isolation of cross-linked products from complex mixtures, boosting their detectability by MS (33–35, 40–42). A second class of cross-linkers containing MS-cleavable bonds have proven to be effective in facilitating the unambiguous identification of cross-linked peptides (36–39, 43, 44), as the resulting cross-linked products can be identified based on their characteristic and simplified fragmentation behavior during MS analysis. Therefore, an ideal cross-linking reagent would possess the combined features of both classes of cross-linkers. To advance the study of in vivo PPIs, we have developed a new XL-MS platform based on a novel membrane-permeable, enrichable, and MS-cleavable cross-linker, Azide-A-DSBSO (azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide), and multistage tandem mass spectrometry (MSⁿ). This new XL-MS strategy has been successfully employed to map in vivo PPIs from mammalian cells at both the proteome scale and the targeted protein complex level.