Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Endoplasmic reticulum export sites and Golgi bodies behave as single mobile secretory units in plant cells

In contrast with animals, plant cells contain multiple mobile Golgi stacks distributed over the entire cytoplasm. However, the distribution and dynamics of protein export sites on the plant endoplasmic reticulum (ER) surface have yet to be characterized. A widely accepted model for ER-to-Golgi transport is based on the sequential action of COPII and COPI coat complexes. The COPII complex assembles by the ordered recruitment of cytosolic components on the ER membrane. Here, we have visualized two early components of the COPII machinery, the small GTPase Sar1p and its GTP exchanging factor Sec12p in live tobacco (Nicotiana tabacum) leaf epidermal cells. By in vivo confocal laser scanning microscopy and fluorescence recovery after photobleaching experiments, we show that Sar1p cycles on mobile punctate structures that track with the Golgi bodies in close proximity but contain regions that are physically separated from the Golgi bodies. By contrast, Sec12p is uniformly distributed along the ER network and does not accumulate in these structures, consistent with the fact that Sec12p does not become part of a COPII vesicle. We propose that punctate accumulation of Sar1p represents ER export sites (ERES). The sites may represent a combination of Sar1p-coated ER membranes, nascent COPII membranes, and COPII vectors in transit, which have yet to lose their coats. ERES can be induced by overproducing Golgi membrane proteins but not soluble bulk-flow cargos. Few punctate Sar1p loci were observed that are independent of Golgi bodies, and these may be nascent ERES. The vast majority of ERES form secretory units that move along the surface of the ER together with the Golgi bodies, but movement does not influence the rate of cargo transport between these two organelles. Moreover, we could demonstrate using the drug brefeldin A that formation of ERES is strictly dependent on a functional retrograde transport route from the Golgi apparatus.     

Comparison of PSGL-1 microbead and neutrophil rolling: microvillus elongation stabilizes P-selectin bond clusters

A cell-scaled microbead system was used to analyze the force-dependent kinetics of P-selectin adhesive bonds independent of micromechanical properties of the neutrophil's surface microvilli, an elastic structure on which P-selectin ligand glycoprotein-1 (PSGL-1) is localized. Microvillus extension has been hypothesized in contributing to the dynamic range of leukocyte rolling observed in vivo during inflammatory processes. To evaluate PSGL-1/P-selectin bond kinetics of microbeads and neutrophils, rolling and tethering on P-selectin-coated substrates were compared in a parallel-plate flow chamber. The dissociation rates for PSGL-1 microbeads on P-selectin were briefer than those of neutrophils for any wall shear stress, and increased more rapidly with increasing flow. The microvillus length necessary to reconcile dissociation constants of PSGL-1 microbeads and neutrophils on P-selectin was 0.21 microm at 0.4 dyn/cm2, and increased to 1.58 microm at 2 dyn/cm2. The apparent elastic spring constant of the microvillus ranged from 1340 to 152 pN/microm at 0.4 and 2.0 dyn/cm2 wall shear stress. Scanning electron micrographs of neutrophils rolling on P-selectin confirmed the existence of micrometer-scaled tethers. Fixation of neutrophils to abrogate microvillus elasticity resulted in rolling behavior similar to PSGL-1 microbeads. Our results suggest that microvillus extension during transient PSGL-1/P-selectin bonding may enhance the robustness of neutrophil rolling interactions.     

Dimerization of P-Selectin Glycoprotein Ligand-1 (PSGL-1) Required for Optimal Recognition of P-Selectin

Interactions between P-selectin, expressed on endothelial cells and activated platelets, and its leukocyte ligand, a homodimer termed P-selectin glycoprotein ligand-1 (PSGL-1), mediate the earliest adhesive events during an inflammatory response. To investigate whether dimerization of PSGL-1 is essential for functional interactions with P-selectin, a mutant form of PSGL-1 was generated in which the conserved membrane proximal cysteine was mutated to alanine (designated C320A). Western blotting under both denaturing and native conditions of the C320A PSGL-1 mutant isolated from stably transfected cells revealed expression of only a monomeric form of PSGL-1. In contrast to cells cotransfected with α1-3 fucosyltransferase-VII (FucT-VII) plus PSGL-1, K562 cells expressing FucT-VII plus C320A failed to bind COS cells transfected with P-selectin in a low shear adhesion assay, or to roll on CHO cells transfected with P-selectin under conditions of physiologic flow. In addition, C320A transfectants failed to bind chimeric P-selectin fusion proteins. Both PSGL-1 and C320A were uniformly distributed on the surface of transfected K562 cells. Thus, dimerization of PSGL-1 through the single, conserved, extracellular cysteine is essential for functional recognition of P-selectin.     

Tissue stretch induces nuclear remodeling in connective tissue fibroblasts

Studies in cultured cells have shown that nuclear shape is an important factor influencing nuclear function, and that mechanical forces applied to the cell can directly affect nuclear shape. In a previous study, we demonstrated that stretching of whole mouse subcutaneous tissue causes dynamic cytoskeletal remodeling with perinuclear redistribution of α-actin in fibroblasts within the tissue. We have further shown that the nuclei of these fibroblasts have deep invaginations containing α-actin. In the current study, we hypothesized that tissue stretch would cause nuclear remodeling with a reduced amount of nuclear invagination, measurable as a change in nuclear concavity. Subcutaneous areolar connective tissue samples were excised from 28 mice and randomized to either tissue stretch or no stretch for 30 min, then examined with histochemistry and confocal microscopy. In stretched tissue (vs. non-stretched), fibroblast nuclei had a larger cross-sectional area (P < 0.001), smaller thickness (P < 0.03) in the plane of the tissue, and smaller relative concavity (P < 0.005) indicating an increase in nuclear convexity. The stretch-induced loss of invaginations may have important influences on gene expression, RNA trafficking and/or cell differentiation.     

Root, shoot tissues of Brassica juncea and Cereal secale promote potato health

Brassica species are increasingly being used as cover crops to suppress soil-borne diseases in potato cropping systems. Experiments were conducted in controlled environments and in the field to evaluate the effects of cover crop root or shoot or a combination of root and shoot tissues on potato root and tuber health. In a lab assay we examined the extent to which volatile compounds released from tissues of two cover crop species, rye (Cereale secale L.) and oriental mustard (Brassica juncea L.), could inhibit mycelium growth of two important potato diseases, Rhizoctonia solani and Pythium ultimum. Twenty-four hours into the lab assay, volatile compounds from all residues suppressed fungal growth. After 48 h, marked suppression of hyphal growth continued in the presence of mustard residues but not in the presence of rye tissues or the control without tissues. A 75 L volume container experiment evaluated the effect of incorporating different quantities of mustard shoot and root tissues (none, comparable to field level and fourfold field level) into R. solani and P. ultimum infested soil on potato growth, root health and tuber disease. In the container study, incorporating mustard shoots at the highest dose increased potato yield by 54% and reduced disease rating to 2.3 compared to a severe rating of 4.4 in the control. In the field trial, potato growth, root health and tuber disease levels were evaluated in plots where disease management involved either incorporation of mustard or rye cover crop roots, shoots and whole plants (roots plus shoots) or standard farmer practice of a fumigated fallow as a control. White root tissue was used as a health indicator, and averaged 58 and 78% in the fumigated control and mustard cover crop treatments, respectively. The highest healthy root tissue status (91%) was recorded where whole plants of mustard were incorporated. In contrast to the visual assessment of root and tuber health, tuber yield in the field was not influenced by cover crop treatment. Across experiments, the incorporation of or exposure to whole mustard plants was consistently effective at suppressing soil-borne fungi and promoting healthy roots and tubers, especially at higher rates of biomass. Mustard should be managed so as to maximize incorporated biomass for effective biofumigation. Multipurpose management requiring removal of mustard shoots is incompatible with promoting potato rhizosphere health.     

The organization of engaged and quiescent translocons in the endoplasmic reticulum of mammalian cells

Protein translocons of the mammalian endoplasmic reticulum are composed of numerous functional components whose organization during different stages of the transport cycle in vivo remains poorly understood. We have developed generally applicable methods based on fluorescence resonance energy transfer (FRET) to probe the relative proximities of endogenously expressed translocon components in cells. Examination of substrate-engaged translocons revealed oligomeric assemblies of the Sec61 complex that were associated to varying degrees with other essential components including the signal recognition particle receptor TRAM and the TRAP complex. Remarkably, these components not only remained assembled but also had a similar, yet distinguishable, organization both during and after nascent chain translocation. The persistence of preassembled and complete translocons between successive rounds of transport may facilitate highly efficient translocation in vivo despite temporal constraints imposed by ongoing translation and a crowded cellular environment.     

Acyl Editing and Headgroup Exchange Are the Major Mechanisms That Direct Polyunsaturated Fatty Acid Flux into Triacylglycerols

Triacylglycerols (TAG) in seeds of Arabidopsis (Arabidopsis thaliana) and many plant species contain large amounts of polyunsaturated fatty acids (PUFA). These PUFA are synthesized on the membrane lipid phosphatidylcholine (PC). However, the exact mechanisms of how fatty acids enter PC and how they are removed from PC after being modified to participate in the TAG assembly are unclear, nor are the identities of the key enzymes/genes that control these fluxes known. By reverse genetics and metabolic labeling experiments, we demonstrate that two genes encoding the lysophosphatidylcholine acyltransferases LPCAT1 and LPCAT2 in Arabidopsis control the previously identified “acyl-editing” process, the main entry of fatty acids into PC. The lpcat1/lpcat2 mutant showed increased contents of very-long-chain fatty acids and decreased PUFA in TAG and the accumulation of small amounts of lysophosphatidylcholine in developing seeds revealed by [¹⁴C]acetate-labeling experiments. We also showed that mutations in LPCATs and the PC diacylglycerol cholinephosphotransferase in the reduced oleate desaturation1 (rod1)/lpcat1/lpcat2 mutant resulted in a drastic reduction of PUFA content in seed TAG, accumulating only one-third of the wild-type level. These results indicate that PC acyl editing and phosphocholine headgroup exchange between PC and diacylglycerols control the majority of acyl fluxes through PC to provide PUFA for TAG synthesis.Plant oils are an important natural resource to meet the increasing demands of food, feed, biofuel, and industrial applications (Lu et al., 2011; Snapp and Lu, 2012). The fatty acid composition in the triacylglycerols (TAG), especially the contents of polyunsaturated fatty acids (PUFA) or other specialized structures, such as hydroxy, epoxy, or conjugated groups, determines the properties and thus the uses of plant oils (Dyer and Mullen, 2008; Dyer et al., 2008; Pinzi et al., 2009; Riediger et al., 2009). To effectively modify seed oils tailored for different uses, it is necessary to understand the fundamental aspects of how plant fatty acids are synthesized and accumulated in seed oils.In developing oilseeds, fatty acids are synthesized in plastids and are exported into the cytosol mainly as oleic acid, 18:1 (carbon number:double bonds), and a small amount of palmitic acid (16:0) and stearic acid (18:0; Ohlrogge and Browse, 1995). Further modification of 18:1 occurs on the endoplasmic reticulum in two major pathways (Fig. 1): (1) the 18:1-CoA may be elongated into 20:1- to 22:1-CoA esters by a fatty acid elongase, FAE1 (Kunst et al., 1992); (2) the dominant flux of 18:1 in many oilseeds is to enter the membrane lipid phosphatidylcholine (PC; Shanklin and Cahoon, 1998; Bates and Browse, 2012), where they can be desaturated by the endoplasmic reticulum-localized fatty acid desaturases including the oleate desaturase, FAD2, and the linoleate desaturase, FAD3, to produce the polyunsaturated linoleic acid (18:2) and α-linolenic acid (18:3; Browse et al., 1993; Okuley et al., 1994). The PUFA may be removed from PC to enter the acyl-CoA pool, or PUFA-rich diacylglycerol (DAG) may be derived from PC by removal of the phosphocholine headgroup (Bates and Browse, 2012). The PUFA-rich TAG are then produced from de novo-synthesized DAG or PC-derived DAG (Bates and Browse, 2012) and PUFA-CoA by the acyl-CoA:diacylglycerol acyltransferases (DGAT; Hobbs et al., 1999; Zou et al., 1999). Alternatively, PUFA may be directly transferred from PC onto DAG to form TAG by an acyl-CoA-independent phospholipid:diacylglycerol acyltransferase (PDAT; Dahlqvist et al., 2000). Recent results demonstrated that DGAT and PDAT are responsible for the majority of TAG synthesized in Arabidopsis (Arabidopsis thaliana) seeds (Zhang et al., 2009).Open in a separate windowFigure 1.Reactions involved in the flux of fatty acids into TAG. De novo glycerolipid synthesis is shown in white arrows, acyl transfer reactions are indicated by dashed lines, and the movement of the lipid glycerol backbone through the pathway is shown in solid lines. Major reactions (in thick lines) controlling the flux of fatty acid from PC into TAG are as follows: LPC acylation reaction of acyl editing by LPCAT (A); PC deacylation reaction of acyl editing by the reverse action of LPCAT or phospholipase A (B); and the interconversion of DAG and PC by PDCT (C). Substrates are in boldface, enzymatic reactions are in italics. FAD, Fatty acid desaturase; FAS, fatty acid synthase; GPAT, acyl-CoA:G3P acyltransferase; LPA, lysophosphatidic acid; LPAT, acyl-CoA:LPA acyltransferase; PA, phosphatidic acid; PLC, phospholipase C; PLD, phospholipase D.The above TAG synthesis model highlights the importance of acyl fluxes through PC for PUFA enrichment in plant oils. However, the exact mechanisms of how fatty acids enter PC and how they are removed from PC after being modified to participate in the TAG assembly are unclear, nor are the identities of the enzymes/genes that control these fluxes known. The traditional view is that 18:1 enters PC through de novo glycerolipid synthesis (Fig. 1; Kennedy, 1961): the sequential acylation of glycerol-3-phosphate (G3P) at the sn-1 and sn-2 positions produces phosphatidic acid; subsequent removal of the phosphate group at the sn-3 position of phosphatidic acid by phosphatidic acid phosphatases (PAPs) produces de novo DAG; finally, PC is formed from DAG by a cytidine-5′-diphosphocholine:diacylglycerol cholinephosphotransferase (CPT; Slack et al., 1983; Goode and Dewey, 1999). However, metabolic labeling experiments in many different plant tissues by us and others (Williams et al., 2000; Bates et al., 2007, 2009; Bates and Browse, 2012; Tjellström et al., 2012) have demonstrated that the majority of newly synthesized fatty acids (e.g. 18:1) enter PC by a process termed “acyl editing” rather than by proceeding through de novo PC synthesis. Acyl editing is a deacylation-reacylation cycle of PC that exchanges the fatty acids on PC with fatty acids in the acyl-CoA pool (Fig. 1, A and B). Through acyl editing, newly synthesized 18:1 can be incorporated into PC for desaturation and PUFA can be released from PC to the acyl-CoA pool to be utilized for glycerolipid synthesis.Additionally, there is accumulating evidence that many plants utilize PC-derived DAG to synthesize TAG laden with PUFA (Bates and Browse, 2012). PC-derived DAG may be synthesized through the reverse reaction of the CPT (Slack et al., 1983, 1985) or by the phospholipases C and D (followed by PAP). However, our recent discovery indicates that the main PC-to-DAG conversion is catalyzed by a phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT) through the phosphocholine headgroup exchange between PC and DAG (Fig. 1C; Lu et al., 2009; Hu et al., 2012). The PDCT is encoded by the REDUCED OLEATE DESATURATION1 (ROD1) gene (At3g15820) in Arabidopsis, which is responsible for about 40% of the flux of PUFA from PC through DAG into TAG synthesis (Lu et al., 2009). Acyl editing and PC-DAG interconversion through PDCT may work together to generate PUFA-rich TAG in oilseed plants (Bates and Browse, 2012).The enzymes/genes involved in the incorporation of 18:1 into PC through acyl editing are not known. However, stereochemical localization of newly synthesized fatty acid incorporation into PC predominantly at the sn-2 position (Bates et al., 2007, 2009; Tjellström et al., 2012) strongly suggest that the acyl editing cycle proceeds through the acylation of lysophosphatidylcholine (LPC) by acyl-CoA:lysophosphatidylcholine acyltransferases (LPCATs [Enzyme Commission 2.3.1.23]; Fig. 1A). High LPCAT activity has been detected in many different oilseed plants that accumulate large amounts of PUFA in TAG (Stymne and Stobart, 1987; Bates and Browse, 2012), suggesting the potential ubiquitous involvement of LPCAT in the generation of PUFA-rich TAG. Several possible pathways for the removal of acyl groups from PC to generate the lysophosphatidylcholine within the acyl editing cycle have been proposed. The acyl groups may be released from PC to enter the acyl-CoA pool via the reverse reactions of LPCATs (Stymne and Stobart, 1984) or by reactions of phospholipase A (Chen et al., 2011) followed by the acyl-CoA synthetases (Shockey et al., 2002). The main focus of this study was to identify the genes and enzymes involved in the incorporation of fatty acids into PC through acyl editing in Arabidopsis and to quantify the contribution of acyl editing and PDCT-based PC-DAG interconversion to controlling the flux of PUFA from PC into TAG. Herein, we demonstrate that mutants of two Arabidopsis genes encoding LPCATs (At1g12640 [LPCAT1] and At1g63050 [LPCAT2]) have reduced TAG PUFA content. Analysis of the acyl-editing cycle through metabolic labeling of developing seeds with [¹⁴C]acetate indicate that the lpcat1/lpcat2 double mutant was devoid of acyl editing-based incorporation of newly synthesized fatty acids into PC, indicating that these two genes are responsible for the acylation of LPC during acyl editing. Additionally, the triple mutant rod1/lpcat1/lpcat2 indicated that PDCT-based PC-DAG interconversion and acyl editing together provide two-thirds of the flux of PUFA from PC to TAG in Arabidopsis seeds.