Exploring the raison d'etre behind metric selection in network analysis: a systematic review.

Network analysis is a useful tool to analyse the interactions and structure of graphs that represent the relationships among entities, such as sectors within an urban system. Connecting entities in this way is vital in understanding the complexity of the modern world, and how to navigate these complexities during an event. However, the field of network analysis has grown rapidly since the 1970s to produce a vast array of available metrics that describe different graph properties. This diversity allows network analysis to be applied across myriad research domains and contexts, however widespread applications have produced polysemic metrics. Challenges arise in identifying which method of network analysis to adopt, which metrics to choose, and how many are suitable. This paper undertakes a structured review of literature to provide clarity on raison d'etre behind metric selection and suggests a way forward for applied network analysis. It is essential that future studies explicitly report the rationale behind metric choice and describe how the mathematics relates to target concepts and themes. An exploratory metric analysis is an important step in identifying the most important metrics and understanding redundant ones. Finally, where applicable, one should select an optimal number of metrics that describe the network both locally and globally, so as to understand the interactions and structure as holistically as possible. Supplementary Information: The online version contains supplementary material available at 10.1007/s41109-022-00476-w.

Structural requirements for ligand binding by a probable plant vacuolar sorting receptor.

How sorting receptors recognize amino acid determinants on polypeptide ligands and respond to pH changes for ligand binding or release is unknown. The plant vacuolar sorting receptor BP-80 binds polypeptide ligands with a central Asn-Pro-Ile-Arg (NPIR) motif. tBP-80, a soluble form of the receptor lacking transmembrane and cytoplasmic sequences, binds the peptide SSSFADSNPIRPVTDRAASTYC as a monomer with a specificity indistinguishable from that of BP-80. tBP-80 contains an N-terminal region homologous to ReMembR-H2 (RMR) protein lumenal domains, a unique central region, and three C-terminal epidermal growth factor (EGF) repeats. By protease digestion of purified secreted tBP-80, and from ligand binding studies with a secreted protein lacking the EGF repeats, we defined three protease-resistant structural domains: an N-terminal/RMR homology domain connected to a central domain, which together determine the NPIR-specific ligand binding site, and a C-terminal EGF repeat domain that alters the conformation of the other two domains to enhance ligand binding. A fragment representing the central domain plus the C-terminal domain could bind ligand but was not specific for NPIR. These results indicate that two tBP-80 binding sites recognize two separate ligand determinants: a non-NPIR site defined by the central domain-EGF repeat domain structure and an NPIR-specific site contributed by the interaction of the N-terminal/RMR homology domain and the central domain.

Molecular cloning and further characterization of a probable plant vacuolar sorting receptor.

BP-80 is a type I integral membrane protein abundant in pea (Pisum sativum) clathrin-coated vesicles (CCVs) that binds with high affinity to vacuole-targeting determinants containing asparagine-proline-isoleucine-arginine. Here we present results from cDNA cloning and studies of its intracellular localization. Its sequence and sequences of homologs from Arabidopsis, rice (Oryza sativa), and maize (Zea mays) define a novel family of proteins unique to plants that is highly conserved in both monocotyledons and dicotyledons. The BP-80 protein is present in dilated ends of Golgi cisternae and in "prevacuoles," which are small vacuoles separate from but capable of fusing with lytic vacuoles. Its cytoplasmic tail contains a Tyr-X-X-hydrophobic residue motif associated with transmembrane proteins incorporated into CCVs. When transiently expressed in tobacco (Nicotiana tabacum) suspension-culture protoplasts, a truncated form lacking transmembrane and cytoplasmic domains was secreted. These results, coupled with previous studies of ligand-binding specificity and pH dependence, strongly support our hypothesis that BP-80 is a vacuolar sorting receptor that trafficks in CCVs between Golgi and a newly described prevacuolar compartment.

Interaction of a potential vacuolar targeting receptor with amino- and carboxyl-terminal targeting determinants.

A protein of 80 kD from developing pea (Pisum sativum) cotyledons has previously been shown to exhibit characteristics of a vacuolar targeting receptor by means of its affinity for the amino-terminal vacuolar targeting sequence of proaleurain from barley (Hordeum vulgare). In this report we show that the same protein also binds to the amino-terminal targeting peptide of prosporamin from sweet potato (Ipomoea batatas) and to the carboxyl-terminal targeting determinant of pro-2S albumin from Brazil nut (Bertholletia excelsa). The receptor protein does not bind to the carboxyl-terminal propeptide (representing the targeting sequence) of barley lectin. The binding of the 80-kD protein to the sporamin determinant involves a motif (NPIR) that has been shown to be crucial for vacuolar targeting in vivo. The binding to the carboxyl-terminal targeting determinant of pro-2S albumin appears to involve the carboxyl-terminal propeptide and the adjacent five amino acids of the mature protein. The 80-kD protein does not bind to peptide sequences that have been shown to be incompetent in directing vacuolar targeting.

Purification and initial characterization of a potential plant vacuolar targeting receptor.

Clathrin-coated vesicles are known to be involved in the transport of proteins from the Golgi to the vacuole in plant cells. The mechanisms by which proteins are directed into this pathway are not known. Here we identify an integral membrane protein of approximately 80 kDa, extracted from clathrin-coated vesicles of developing pea (Pisum sativum L.) cotyledons, that bound at neutral pH to an affinity column prepared with the N-terminal targeting determinant of the vacuolar thiol protease, proaleurain, and eluted when the pH was lowered to 4. The protein was not retained on a control column prepared with the N-terminal sequence of a homologous, secreted thiol protease, endopeptidase B. The 80-kDa protein also accumulated in a membrane fraction that is less dense than clathrin-coated vesicles. In vitro studies demonstrated a binding constant of 37 nM between the approximately 80 kDa protein and the proaleurain targeting determinant. A peptide with a vacuolar targeting determinant from prosporamin weakly competed for binding to the approximately-80 kDa protein, while a peptide carrying a single amino acid substitution known to abolish prosporamin vacuolar targeting had no measurable binding affinity for the protein. The binding protein is a glycoprotein with a transmembrane orientation in which the C terminus is exposed to the cytoplasm. The binding domain is located in the N-terminal luminal portion of the protein. These properties of the binding protein are consistent with the function of a receptor that would select proteins in the trans-Golgi for sorting to clathrin-coated vesicles and delivery to the vacuole.

Uncoating of clathrin-coated vesicles by uncoating ATPase from developing peas.

A cytosolic ATPase (an enzyme that dissociates clathrin from clathrin-coated vesicles in the presence of ATP) was isolated from developing pea (Pisum sativum L.) cotyledons using chromatography on ATP-agarose. After chromatography on phenyl Sepharose, the fraction with uncoating activity was enriched in a doublet of 70-kD peptides. Using chromatofocusing, it was possible to produce fractions enriched in the upper component of the doublet of 70-kD peptides; these fractions still retained ATP-dependent uncoating activity. In western blot analysis, antibodies against a member of the 70-kD family of heat-shock proteins interacted with the upper component of the doublet of the 70-kD peptides from the phenyl Sepharose-purified fractions. On the basis of these data, it appears that the uncoating ATPase may be a member of the 70-kD family of heat-shock proteins. The uncoating activity removed clathrin from both pea and bovine brain clathrin-coated vesicles. The uncoating ATPase from bovine brain also uncoated coated vesicles from peas. Pea clathrin-coated vesicles that were prepared by three different methods were uncoated to different extents by the plant uncoating ATPase. Different populations of clathrin-coated vesicles from the same preparation showed differential sensitivity to the uncoating ATPase. Limited proteolysis of the clathrin light chains in the protein coat abolished the susceptibility of the clathrin-coated vesicles to the uncoating ATPase. The properties of the uncoating ATPase isolated from developing pea cotyledons are similar to those of uncoating ATPases previously described from mammalian and yeast systems. It appears that despite dissimilarities in composition of the clathrin components of the vesicles from the respective sources, uncoating is achieved by a common mechanism.

Characterization of tonoplast polypeptides isolated from corn seedling roots.

Tonoplast vesicles were isolated by discontinuous sucrose gradient centrifugation in the presence of Mg(2+) from 5 day old corn (Zea mays L., Golden Cross Bantam) seedling roots. Marker enzyme assays indicated only a low degree of cross-contamination of tonoplast vesicles at the 10/23% (weight/weight) interface by other membrane components. Severalfold enrichment of tonoplast ATPase and pyrophosphatase was indicated in tonoplast fractions by dot blot studies with antibodies against an oat tonoplast ATPase and a mung bean tonoplast pyrophosphatase. Comparison of two-dimensional electrophoretic gels of tonoplast and microsomal membrane polypeptides revealed approximately 68 polypeptides to be specific to tonoplast by silver staining. Immunoblot analysis with antibodies against a tonoplast holoenzyme ATPase from oat roots revealed the presence of the 72, 60, and 41 kilodalton polypeptides in isolated tonoplast vesicles from corn roots. Affinity blotting with concanavalin A and secondary antibodies indicated the degree of glycosylation of tonoplast polypeptides, where 21 of 68 tonoplast-specific polypeptides contained detectable carbohydrate moieties. Salt and NaOH washes removed 38 of the tonoplast-specific polypeptides, indicating a peripheral association with the membrane. Thirteen of the peripheral polypeptides and eight of the integral polypeptides were identified as glycoproteins. This information on the polypeptide composition of the tonoplast of root cells will aid in gaining insight into the role of this membrane in controlling vacuolar functions.

Essential arginine residues in the nitrate uptake system from corn seedling roots.

Three dicarbonyl reagents were used to demonstrate the presence of an essential arginine residue in the NO(3) (-) uptake system from corn seedling roots (Zea mays L., Golden Cross Bantam). Incubation of corn seedlings with 2,3-butanedione (0.125-1.0 millimolar) and 1,2-cyclohexanedione (0.5-4.0 millimolar) in the presence of borate or with phenylglyoxal (0.25-2.0 millimolar) at pH 7.0 and 30 degrees C resulted in a time-dependent loss of NO(3) (-) uptake following pseudo-first-order kinetics. Second-order rate constants obtained from slopes of linear plots of pseudo-first-order rate constants versus reagent concentrations were 1.67 x 10(-2), 0.68 x 10(-2), and 1.00 x 10(-2) millimolar per minute for 2,3-butanedione, 1,2-cyclohexanedione, and phenylglyoxal, respectively, indicating the faster rate of inactivation with 2,3-butanedione at equimolar concentration. Double log plots of pseudo-first-order rate constants versus reagent concentrations yielded slope values of 1.031 (2,3-butanedione), 1.004 (1,2-cyclohexanedione), and 1.067 (phenylglyoxal), respectively, suggesting the modification of a single arginine residue. The effectiveness of the dicarbonyl reagents appeared to increase with increasing medium pH from 5.5 to 8.0. Unaltered K(m) and decreased V(max) in the presence of reagents indicate the inactivation of the modified carriers with unaltered properties. The results thus obtained indicate that the NO(3) (-) transport system possesses at least one essential arginine residue.

Coated Vesicles Are Involved in the Transport of Storage Proteins during Seed Development in Pisum sativum L.

During seed development, various storage proteins and hydrolases accumulate in specialized storage vacuoles, the protein bodies, via an elaborate intracellular transport system involving the rough endoplasmic reticulum, the Golgi apparatus, and transit vesicles. Clathrin-coated vesicles, similar to those which transport lysosomal proteins to lysosomes, an organelle analogous to the vacuole, in animal cells, could be involved in this intracellular transport mechanism. Clathrin-coated vesicles have been isolated from cotyledons of developing pea (Pisum sativum L.) seeds at the time of rapid protein accumulation and analyzed for the presence of protein body constitutents. A 23,000 M(r) polypeptide, corresponding to pea lectin precursor, was found associated with the vesicles, as determined by immunoblotting. The lectin precursor was apparently sequestered within the vesicles, as the polypeptide was only susceptible to proteolysis if detergents were included in the digestion buffer. A number of glycosidase activities, including alpha-mannosidase, alpha-galactosidase, and beta-N-acetylhexosaminidase, were also associated with the vesicles. Thus, it appears that clathrin-coated vesicles are involved in the intracellular transport of storage proteins during seed development.

Isozymes of beta-N-Acetylhexosaminidase from Pea Seeds (Pisum sativum L.).

Four isozymes of beta-N-acetylhexosaminidase (beta-NAHA) from pea seeds (Pisum sativum L.) have been separated, with one, designated beta-NAHA-II, purified to apparent homogeneity by means of an affinity column constructed by ligating p-aminophenyl-N-acetyl-beta-d-thioglucosaminide to Affi-Gel 202. The other three isozymes have been separated and purified 500- to 1750-fold by chromatography on Concanavalin A-Sepharose, Zn(2+) charged immobilized metal affinity chromatography, hydrophobic chromatography, and ion exchange chromatography on CM-Sephadex. All four isozymes are located in the protein bodies of the cotyledons. The molecular weight of each isozyme is 210,000. beta-NAHA-II is composed of two heterogenous subunits. The subunits are not held together by disulfide bonds, but sulfhydryl groups are important for catalysis. All four isozymes release p-nitrophenol from both p-nitrophenyl-N-acetyl-beta-d-glucosaminide and p-nitrophenyl-N-acetyl-beta-d-galactosaminide. The ratio of activity for hydrolysis of the two substrates is pH dependent. The K(m) value for the two substrates and pH optima of the isozymes are comparable to beta-NAHAs from other plant sources.

Regulation of nitrite reductase : cell-free translation and processing.

A protein with molecular mass of 67 kilodaltons is immunoprecipitated from in vitro translated products obtained from rabbit reticulocyte lysate primed with polyadenylated RNA from nitrate treated illuminated pea seedlings. This protein resembles the native nitrite reductase because of its competitive elimination when immunoprecipitation of in vitro translated products was carried out in the presence of cold unlabeled nitrite reductase or in vivo labeled pea leaf extract. This protein is of slightly higher molecular weight than that of the native nitrite reductase. Proteinaceous extracts from chloroplasts convert the in vitro product to the same molecular weight as the native peptide. The conversion appears to occur in two steps. Polyadenylated RNA from nitrate deficient plants or from nitrate-treated plants transferred to darkness do not support the synthesis of nitrite reductase. It is concluded that nitrate and light modulate the synthesis of the enzyme nitrite reductase by regulating the availability of mRNA for the enzyme.

Regulation of synthesis of nitrite reductase in pea leaves: in-vivo and in-vitro studies.

Crude protein extracts from leaves of pea (Pisum sativum L.) labeled with an L-(14)C-amino-acid mixture or [(35)S]methionine, were treated with antibodies prepared against nitrite reductase (NiR; EC 1.6.6.4). When the immunoprecipitates were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) a polypeptide with the same mobility as that of the native NiR was detected. By using darkened or illuminated leaves in the absence or presence of nitrate, it has been confirmed that nitrate is required in the in-vivo synthesis of NiR and that this synthesis is stimulated by light. Cell-free translation with a wheat-germ extract primed with polysomes from illuminated leaves treated with nitrate yielded polypeptides of a wide range of molecular weights (Mrs). Two polypeptides were immunoprecipitated from the translational products by anti-NiR serum. The mobility of one of them on SDS-PAGE corresponded to that of NiR while the other had a slightly higher Mr. It is concluded that NiR is synthesized as a heavy-molecular-weight precursor. Nitrate appears to regulate NiR synthesis by triggering transcription whereas the light may control the level of transcription or translation.

Protein bodies and vacuoles as lysosomes : investigations into the role of mannose-6-phosphate in intracellular transport of glycosidases in pea cotyledons.

We have failed to detect the presence of mannose-6-phosphate in the oligosaccharide moiety of glycoproteins from pea (Pisum sativum L. cv Burpeeana) cotyledons using an assay system sensitive to 10 picomoles of mannose-6-phosphate. We were also unable to demonstrate any retention of glycosidase activity from pea seedlings and pea cotyledons on Sepharose-coupled phosphomannosyl receptor proteins isolated from bovine liver which were, however, able to retain phosphomannosylated hexosaminidase purified from Dictyostelium discoideum secretions. Furthermore, although Sepharose-coupled phosphomannosylated hexosaminidase from Dictyostelium was able to bind phosphomannosyl receptors from bovine liver we were unable to detect the retention of any protein from acetone powder extracts of pea seedlings or from endoplasmic reticulum-associated proteins of pea cotyledons.Based on this collective evidence we conclude that mannose-6-phosphate does not appear to play a role in the targeting of hydrolytic enzymes from the endoplasmic reticulum to the protein bodies in pea cotyledons.

Synthesis and degradation of nitrite reductase in pea leaves.

We have shown in a previous publication (Gupta, Beevers 1983 J Exp Bot 34: 1455-1462) that the level of extractable nitrite reductase activity in pea (Pisum sativum cv Burpeeana) leaves is subject to environmental perturbations. In the current study, we have used rocket immunoelectrophoresis to quantitate the level of nitrite reductase protein in extracts from pea plants subjected to various environmental treatments. The level of nitrite reductase cross-reacting material closely followed the level of assayable nitrite reductase activity. The environmental conditions which enhanced the level of extractable nitrite reductase activity resulted in an increased level of nitrite reductase cross-reacting material in the extracts. In contrast, environmental conditions which resulted in a decrease in the level of extractable nitrite reductase activity produced a decline in cross-reacting material. These results indicate that the environmentally induced modulation of extractable nitrite reductase activity involves alteration of enzyme level and is not mediated by a reversible activation-inactivation of the existing enzyme.

Sequestration of pea reserve proteins by rough microsomes.

Free polysomes, polysomes released from membranes, and rough microsomal vesicles isolated from developing cotyledons of Pisum sativum L. cv. Burpeeana were used to direct cell-free protein synthesis in a wheat germ system. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated that the polypeptide products had molecular weights ranging from 12,000 to 74,000. Some of the polypeptides migrated during electrophoresis with the same mobility as polypeptides present in legumin and vicilin preparations. By the use of rabbit antibodies raised against pea reserve proteins it was established that polysomes released from membranes and rough microsomes directed the synthesis of polypeptides that were related to reserve proteins whereas free polysomes did not.Centrifugation studies indicated that the majority of the radioactivity incorporated by rough microsomes was specifically associated with the microsomes. The incorporated radioactivity of sedimented microsomes was not released by treatment with KCl and was resistant to proteolysis unless detergent was present. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the sequestered translation products were related to pea reserve proteins. It is concluded that the reserve proteins of pea cotyledons are synthesized exclusively by membrane-bound polysomes and that they are sequestered within the rough endoplasmic reticulum.

Incorporation of [C]Glucosamine and [C]Mannose into Glycolipids and Glycoproteins in Cotyledons of Pisum sativum L.

Developing pea cotyledons incorporate radioactivity in vivo from [(14)C]glucosamine and [(14)C]mannose into glycolipids and glycoproteins. Several different lipid components are labeled including neutral, ionicnonacidic, and acidic lipids. The acidic lipids labeled in vivo appear similar to the polyisoprenoid lipid intermediates formed in vitro in pea cotyledons. Radioactivity from [(14)C]glucosamine and [(14)C]mannose is also incorporated into glycopeptides. Considerable redistribution of [(14)C]mannose into other glycosyl components found in endogenous glycoproteins is observed. An N-acetylglucosamine to asparagine glycopeptide linkage has been isolated from [(14)C]glucosamine-labeled glycoproteins.

Glycosylation of pea cotyledon membranes.

Pea cotyledons were injected with d-[(14)C]mannose or d-[(14)C]-glucosamine and incubated for 1 to 1.5 hours. Cotyledons were homogenized and subcellular fractions were isolated by differential centrifugation followed by linear sucrose density gradient centrifugation.Radioactivity that was precipitated by trichloroacetic acid was associated most extensively with rough endoplasmic reticulum, Golgi membranes, a membrane with a density of 1.14 grams per cubic centimeter (possibly plasma membrane) and an unidentified subcellular component with a density of 1.22 grams per cubic centimeter. Lower levels of incorporation were observed in protein bodies and mitochondria.Isolated membrane fractions were lipid-extracted to determine which components of the membrane contained the label. Rough endoplasmic reticulum contained the most extensively labeled lipids which had similar properties to the lipid intermediates thought to be involved in glycoprotein assembly. The lipid free residues of the various membrane fractions contained radioactivity that was released by protease treatment. Acid hydrolysis of the residues indicated that most of the radioactivity was associated with mannose or glucosamine. It appears that various subcellular components of the pea cotyledon possess glycoproteins that contain mannose and glucosamine.

What is pea legumin - Is it glycosylated?

Since there is some question as to whether or not legumin is glycosylated, this storage protein was isolated by various procedures from developing cotyledons of Pisum sativum L. supplied with [(14)C]-labeled glucosamine and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis. Legumin isolated by the classical method of Danielsson [(1949) Biochem. J. 44, 387-400] a procedure in which globulins extracted with a buffered salt solution are precipitated with ammonium sulfate (70% saturation) and legumin separated from vicilin by isoelectric precipitation, was labeled. The glucosamine incorporated into legumin was associated with low-molecular-weight polypeptides. In contrast, legumin isolated by the method of Casey [(1979) Biochem. J. 177, 509-520], a procedure where legumin is prepared by zonal isoelectric precipitation from globulins precipitated with 40-70% ammonium sulfate, was not labeled. However, the globulin fraction precipitated with 40% ammonium sulfate was labeled and the radioactive glucosamine was associated with low-molecular-weight polypeptides. Legumin isolated from protein bodies [Thomson et al. (1978) Aust. J. Plant Physiol. 5, 263-279] was not extensively labeled. However, the saltinsoluble fraction of protein body extracts was labeled and the radioactivity was associated with low-molecular-weight polypeptides. These results indicate that protein bodies contain a glycoprotein of low-molecular-weight that co-purifies with legumin isolated by the method of Danielsson but that is discarded when isolation methods developed more recently are used.

Membrane-associated Glycosyl Transferases in Cotyledons of Pisum sativum: Differential Effects of Magnesium and Manganese Ions.

In crude particulate fractions isolated from pea (Pisum sativum) cotyledons, the transfer of radioactivity from GDP-[(14)C]mannose to glycolipid appears to be preferentially stimulated by Mn(2+) while the transfer to lipid-free residue is enhanced by Mg(2+). In contrast, the transfer of radioactivity from UDP-N-acetyl-[(14)C]glucosamine to glycolipid shows preferential stimulation by Mg(2+) while the transfer to lipid-free residue prefers Mn(2+). These results are accounted for by the differential stimulation by Mg(2+) and Mn(2+) of glycosyl transferases associated with subcellular membranes which were separated by isopycnic sucrose density centrifugation.