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The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.

Quality protein maize (QPM) is a high lysine-containing corn that is based on genetic modification of the opaque2 (o2) mutant. In QPM, modifier genes convert the starchy endosperm of o2 to the vitreous phenotype of wild type maize. There are multiple, unlinked o2 modifier loci (Opm) in QPM and their nature and mode of action are unknown. We previously identified seven Opm QTLs and characterized 16 genes that are differentially up-regulated at a significant level in K0326Y QPM, compared to the starchy endosperm mutant W64Ao2. In order to further characterize these Opm QTLs and the genes up-regulated in K0326Y QPM, we created a population of 314 recombinant inbred lines (RILs) from a cross between K0326Y QPM and W64Ao2. The RILs were characterized for three traits associated with endosperm texture: vitreousness, density and hardness. Genetic linkage analysis of the RIL population confirmed three of the previously identified QTLs associated with o2 endosperm modification in K0326Y QPM. Many of the genes up-regulated in K0326Y QPM showed substantially higher levels of expression in vitreous compared with opaque RILs. These included genes associated with the upstream regulation of the ethylene response pathway, and a gene encoding a regulatory subunit of pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase, an adaptive enzyme of the glycolytic pathway.

The opaque-2 (o2) mutation of maize increases lysine content, but the low seed density and soft texture of this type of mutant are undesirable. Lines with modifiers of the soft kernel phenotype (mo2) called "Quality Protein Maize" (QPM) have high lysine and kernel phenotypes similar to normal maize. Prior research indicated that the formation of vitreous endosperm in QPM might involve changes in starch granule structure. In this study, we focused on analysis of two starch biosynthetic enzymes that may influence kernel vitreousness. Analysis of recombinant inbred lines derived from a cross of W64Ao2 and K0326Y revealed that pullulanase activity had significant positive correlation with kernel vitreousness. We also found that decreased Starch Synthase III abundance may decrease the pullulanase activity and average glucan chain length given the same Zpu1 genotype. Therefore, Starch Synthase III could indirectly influence the kernel vitreousness by affecting pullulanase activity and coordinating with pullulanase to alter the glucan chain length distribution of amylopectin, resulting in different starch structural properties. The glucan chain length distribution had strong positive correlation with the polydispersity index of glucan chains, which was positively associated with the kernel vitreousness based on nonlinear regression analysis. Therefore, we propose that pullulanase and Starch Synthase III are two important factors responsible for the formation of the vitreous phenotype of QPM endosperms.

Since its development more than two decades ago, Quality Protein Maize (QPM) has been adopted for cultivation in many regions of the developing world. Given the potential benefits of widespread use of QPM, research to better understand the genetic and biochemical mechanisms responsible for its altered kernel texture and protein quality is important. Recent investigations into the improved protein quality of the opaque2 mutant and the genetic mechanisms that can suppress its starchy kernel phenotype provide new insights to support the continued improvement of QPM. Chief among these developments are the use of transgenic approaches to improve nutritional quality and the discovery that an important component of modified endosperm texture in QPM is related to altered starch granule structure.

The biochemical basis of modified kernel texture in Quality Protein Maize (QPM) is poorly understood. Proteomic analysis of several QPM lines indicated increased levels of granule-bound starch synthase I in the soluble nonzein protein fraction of these genotypes. Increased extraction of this enzyme reflected a change in starch structure, which was manifested as shorter amylopectin branches and increased starch-granule swelling. In mature kernels, these alterations in starch structure were associated with interconnections between starch granules that resulted in a vitreous kernel phenotype. Understanding the molecular basis for this previously uncharacterized starch structure will accelerate the development of QPM.

Eukaryotic elongation factor 1A (eEF1A) appears to be a multifunctional protein because several biochemical activities have been described for this protein, in addition to its role in protein synthesis. In maize (Zea mays) endosperm, the synthesis of eEF1A is increased in o2 (opaque2) mutants, and its concentration is highly correlated with the protein-bound lysine content. To understand the basis of this relationship, we purified eEF1A isoforms from developing endosperm and investigated their accumulation and their functional and structural properties. Formation of three isoforms appears to be developmentally regulated and independent of the o2 mutation, although one isoform predominated in one high lysine o2 inbred. The purified proteins differ in their ability to bind F-actin in vitro, suggesting that they are functionally distinct. However, they share similar aminoacyl-tRNA-binding activities. Tandem mass spectrometry revealed that each isoform is composed of the four same gene products, which are modified posttranslationally by methylation and phosphorylation. The chemical differences that account for their different actin-binding activities could not be determined.

Plants are uniquely adapted to respond to environmental and developmental signals for survival. Many signals result in dramatic changes of cell shape or cytoplasmic organization that are dependent on the actin cytoskeleton. The dynamic nature of the actin cytoskeleton is conferred by a wide variety of actin-binding proteins. One class of these proteins is capable of binding to free actin monomers and thereby regulates the polymerization of actin filaments. Two such proteins have been identified in plants: profilin and actin-depolymerizing factor (ADF). These proteins comprise multigene families in plants and the isoforms of each protein have unique developmentally and spatially regulated expression patterns. Biochemical analysis of the plant monomer-binding proteins indicates that they are able to both stimulate and inhibit actin polymerization in vitro. Furthermore, microinjection of these proteins into cells reveals that simple models for the interaction of monomer-binding proteins with actin are inadequate. The complex effects on actin in vitro and in vivo are due to the ability of profilin and ADF to interact with a number of other ligands, such as regulatory proteins and polyphosphoinositide lipids. The monomer-binding proteins also respond to changes in cytosolic Ca 2+ and pH. Regulation of these proteins by phosphorylation adds an additional level of complexity for the study of their role in coordinating actin reorganization in plant cells. A model of actin filament assembly in tip-growing cells that incorporates the activities of profilin and ADF is presented.

Recently it has been established, through a detailed biochemical analysis, that recombinant Arabidopsis thaliana fimbrin 1 (AtFim1) is a member of the fimbrin/plastin family of actin filament bundling or cross-linking proteins [D.R. Kovar et al. (2000) Plant J 24:625-636]. To determine whether AtFim1 can function as an F-actin-binding protein in the complex environment of the plant cell cytoplasm, we created a fluorescent protein analog and introduced it by microinjection into live Tradescantia virginiana L. stamen hair cells. AtFim1 derivatized with Oregon Green 488 had biochemical properties similar to unlabeled fimbrin, including the Kd value for binding to plant F-actin and the ability to cross-link filaments into higher-order structures. Fluorescent-fimbrin decorated an array of fine actin filaments in the cortical cytoplasm of stamen hair cells, which were shown with time-course studies to be highly dynamic. These data establish AtFim1 as a bona fide member of the fimbrin/plastin family, and represent the first use of a plant actin-binding protein as a powerful cytological tool for tracking the spatial and temporal redistribution of actin filaments in individual cells.

Regulation of pollen tube growth is known to involve alterations in intracellular calcium levels and phosphoinositide signaling, although the mechanisms involved are unclear. However, it appears likely that pollination events involve a complex interplay between signaling pathways and components of the actin cytoskeleton in pollen. In many eukaryotic cells, actin binding proteins function as stimulus-response modulators, translating signals into alterations in the cytoplasmic architecture. In this study, we examined whether profilin, which is a member of this class of signaling intermediate, might play a similar role in pollen. We have analyzed the functional properties of native profilin from pollen of Papaver rhoeas and have investigated the effects of profilin on the phosphorylation of pollen proteins in vitro by adding a slight excess of profilin to cytosolic pollen extracts. We present clear evidence that profilin interacts with soluble pollen components, resulting in dramatic alterations in the phosphorylation of several proteins. We also show, albeit in vitro, the involvement of profilin in modulating the activity of a signaling component(s) affecting protein phosphorylation. Our data, which suggest that pollen profilin can regulate actin-based cytoskeletal protein assembly and protein kinase or phosphatase activity, indicate a possible role for the involvement of profilin in signaling pathways that may regulate pollen tube growth.

A vast array of actin binding proteins (ABPs), together with intracellular signaling molecules, modulates the spatiotemporal distribution of actin filaments in eukaryotic cells. To investigate the complex regulation of actin organization in plant cells, we designed experiments to reconstitute actin-ABP interactions in vitro with purified components. Because vertebrate skeletal [alpha]-actin has distinct and unpredictable binding affinity for nonvertebrate ABPs, it is essential that these in vitro studies be performed with purified plant actin. Here, we report the development of a new method for isolating functional actin from maize pollen. The addition of large amounts of recombinant profilin to pollen extracts facilitated the depolymerization of actin filaments and the formation of a profilin-actin complex. The profilin-actin complex was then isolated by affinity chromatography on poly-L-proline-Sepharose, and actin was selectively eluted with a salt wash. Pollen actin was further purified by one cycle of polymerization and depolymerization. The recovery of functional actin by this rapid and convenient procedure was substantial; the average yield was 6 mg of actin from 10 g of pollen. We undertook an initial physicochemical characterization of this native pollen actin. Under physiological conditions, pollen actin polymerized with kinetics similar in quality to those for vertebrate [alpha]-actin and had a critical concentration for assembly of 0.6 [mu]M. Moreover, pollen actin interacted specifically and in a characteristic fashion with several ABPs. Tradescantia cells were microinjected and used as an experimental system to study the behavior of pollen actin in vivo. We demonstrated that purified pollen actin ameliorated the effects of injecting excess profilin into live stamen hair cells.

A striking feature of the eukaryotic actin cytoskeleton is its ability to undergo dramatic reorganization in response to internal and environmental stimuli. In plant cells, several cellular processes depend on, or are coincident with, reorganization of the actin cytoskeleton, including division, differentiation, light-induced plastid migration, wound repair and response to pathogen attack. Understanding how the actin cytoskeleton responds to these internal and extracellular factors requires a detailed understanding of the molecular mechanisms that coordinate actin polymerization and depolymerization. There is increasing evidence that the small actin-binding proteins profilin and actin-depolymerizing factor regulate actin dynamics in plant cells. These proteins may serve to integrate signaling cues and translate this information to remodel the cytoplasmic architecture.

To characterize the function of plant profilins in vivo, we expressed two pollenspecific Zea mays (maize) profilin isoforms in profilin-minus Dictyostelium discoideum mutants. In maize, profilins exist as a multigene family containing 4 or more members which are highly similar to each other but substantially less similar to profilins from animals and lower eukaryotes. Previously we have shown that D. discoideum profilin-minus cells have an aberrant phenotype due to defects in cell shape, cytokinesis, and development. These defects could be rescued by introducing the pollen-specific profilins 1 or 2 from maize using a newly constructed expression vector. Expression of the heterologous profilins in Dictyostelium clones was assayed by affinity purification of the pollen profilins with poly-~proline agarose and by immunoblotting with a polyclonal antiserum raised against maize pollen profilin. In contrast to the profilin-minus mutants, Dictyostelium cells expressing plant profilins showed normal cell shape, contained less F-actin, and were able to form fruiting bodies. These data provide genetic evidence that maize pollen profilins, even though they are specific for a distinct developmental stage, share functional properties with profilin from a lower eukaryote and apparently act as G-actin-sequestering proteins in this system. 0 1996 Wiley-Liss, Inc.

The role of cytosolic pH (pHc) in determining the growth site and in tip elongation has been investigated by measuring and manipulating pHc. pHcacidifies by 0.1–0.2 units as the growth axis is established. Concomitantly, cells accumulate KCl, which increases the cellular osmotic pressure, resulting in the generation of turgor pressure. The K+taken up is apparently compartmentalized as the free cytosolic K+activity remains constant. At present, the relation between pHc, K+, and turgor pressure is not well understood. A small but statistically significant cytosolic pH gradient, acid at the future growth site, is also detectable during axis establishment. As growth is initiated the intensity of the gradient increases to approximately 0.3 pH units. The magnitude of the pH gradient correlates with the rate of tip elongation. The gradient may regulate tip elongation in a number of ways, including local control of the assembly and stability of cytoskeletal elements. Key words: cytosolic pH gradients, tip growth, turgor pressure, weak acids and bases, SNARF 1, pH-sensitive microelectrodes.

We have investigated the role of intracellular pH (pHi) in early plant development using ion-selective microelectrodes to record from eggs and embryos of the brown alga Pelvetia. Temporal changes in pHi were investigated by recording from zygotes at all stages of the first cell cycle. pHi was 7.57 +/- 0.09 in recently fertilized eggs, but decreased by approximately 0.2 units a few hours postfertilization. Proton motive force (pmf) was also monitored and found to be less than -50 mV throughout the first cell cycle. Because of the low pmf values, we suggest that secondary active transport is probably not coupled to H+, and instead we propose that solute transport is driven by the Na+ electrochemical potential. Zygotes strictly regulated pHi over a wide range of extracellular pH (pHo); pHi varied by less than 0.2 units over pHo values from 6.2 to 9.2. Inhibitor studies were conducted to investigate the mechanism of regulation. Agents known to inhibit the H(+)-ATPase (antimycin A, KCN, carbonylcyanide m-chlorophenylhydrazone, N,N'-dicyclohexylcarbodiimide, and erythrosin B) caused marked cytoplasmic acidification. Addition of amiloride, an inhibitor of Na+/H+ antiport, also resulted in acidification, as did removal of NaCl from the medium. By contrast, increasing extracellular NaCl concentration caused transient alkalinization of the cytoplasm. Taken together, these results indicate that proton pumping by an H(+)-ATPase and Na+/H+ antiporter contribute to pH regulation.

Quality protein maize (QPM) was created by selecting genetic modifiers that convert the starchy endosperm of an opaque2 (o2) mutant to a hard, vitreous phenotype. Genetic analysis has shown that there are multiple, unlinked o2 modifiers (Opm), but their identity and mode of action are unknown. Using two independently developed QPM lines, we mapped several major Opm QTLs to chromosomes 1, 7 and 9. A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs. Several of the genes are associated with ethylene and ABA signaling and suggest a potential linkage of o2 endosperm modification with programmed cell death.

A quantitative trait locus has previously been identified in maize (Zea mays L.) that influences the level of free amino acids in the endosperm, especially those from the aspartate pathway: lysine, threonine, methionine, leucine, and isoleucine. Because this locus occurs in a region of the genome containing ask2, a monofunctional aspartate kinase, the nature of the monofunctional aspartate kinase genes in the parental inbreds, Oh545o2 and Oh51Ao2, was investigated. Two genes, Ask1 and Ask2 were isolated, and Ask2 was mapped to the ask2 locus. Nucleotide sequence analysis of the Ask2 alleles from Oh545o2 and Oh51Ao2 showed they differ by one amino acid. Both alleles complemented a yeast aspartate kinase mutant, hom3, and based on the growth of the yeast mutant it appeared that Ask2-Oh545o2 produces an enzyme with greater total activity than that encoded by the Oh51Ao2 allele. The results suggest that the higher level of free amino acids derived from the aspartate pathway in Oh545o2 endosperm results from a single amino acid change in the ASK2 enzyme that has pleiotropic effects on its activity.

Mucronate (Mc) was identified as a dominant maize (Zea mays L.) opaque kernel mutation that alters zein storage protein synthesis. Zein protein bodies in Mc endosperm are misshapen and are associated with increased levels of ER Lumenal Binding Protein (BiP). Using GeneCalling to profile endosperm RNA transcripts, we identified an aberrant RNA in Mc that encodes the 16-kDa gamma-zein protein. The transcript contains a 38-bp deletion (nucleotides 406-444 after the initiation codon) that creates a frame-shift mutation and an abnormal sequence for the last 63 amino acids. Genetic mapping revealed the Mc mutation is linked with the locus encoding the 16-kDa gamma-zein, and two-dimensional gel electrophoresis confirmed the 16-kDa gamma-zein protein is altered in Mc. The mutant protein exhibited changes in solubility properties and co-immunoprecipitated with the molecular chaperone, BiP. Transgenic maize plants expressing the Mc 16-kDa gamma-zein manifested an opaque kernel phenotype with enhanced levels of BiP in the endosperm, similar to the Mc mutant. Unlike the wild-type protein, the Mc 16-kDa gamma-zein interacted only weakly with the 22-kDa alpha-zein when expressed in the yeast two-hybrid system. These results indicate that the Mc phenotype results from a frame-shift mutation in the gene encoding the 16-kDa gamma-zein protein, leading to the unfolded protein response in developing endosperm.

The disposal of misfolded proteins from the lumen of the endoplasmic reticulum (ER) is one of the quality control mechanisms present in the protein secretory pathway. Through ER-associated degradation, misfolded substrates are targeted to the cytosol where they are degraded by the proteasome. We have identified four maize (Zea mays) Der1-like genes (Zm Derlins) that encode homologs of Der1p, a yeast (Saccharomyces cerevisiae) protein implicated in ER-associated degradation. Zm Derlins are capable of functionally complementing a yeast Der1 deletion mutant. Such complementation indicates that the Der1p function is conserved among species. Zm Derlin genes are expressed at low levels throughout the plant, but appear prevalent in tissues with high activity of secretory protein accumulation, including developing endosperm cells. Expression of three of the four Zm Derlin genes increases during ER stress, with Zm Derlin1-1 showing the strongest induction. Subcellular fractionation experiments localized Zm Derlin proteins to the membrane fraction of microsomes. In maize endosperm, Zm Derlin proteins were found primarily associated with ER-derived protein bodies regardless of the presence of an ER stress response.

The opaque2 (o2) mutation increases the Lys content of maize (Zea mays) endosperm by reducing the synthesis of zein storage proteins and increasing the accumulation of other types of cellular proteins. Elongation factor 1A (eEF1A) is one of these proteins, and its concentration is highly correlated with the amount of other Lys-containing proteins in the endosperm. We investigated the basis for this relationship by comparing patterns of protein accumulation and gene expression between a high (Oh51Ao2) and a low (Oh545o2) eEF1A inbred, as well as between high and low eEF1A recombinant inbred lines obtained from their cross. The content of α-zein and several cytoskeletal proteins was measured in high and low eEF1A inbred lines, and the levels of these proteins were found to correlate with that of eEF1A. To extend this analysis, we used an endosperm expressed sequence tag microarray to examine steady-state levels of RNA transcripts in developing endosperm of these genotypes. We identified about 120 genes coordinately regulated in association with eEF1A content. These genes encode proteins involved in several biological structures and processes, including the actin cytoskeleton, the endoplasmic reticulum, and the protein synthesis apparatus. Thus, higher levels of eEF1A in o2 mutants may be related to a more extensive cytoskeletal network surrounding the rough endoplasmic reticulum and increased synthesis of cytoskeleton-associated proteins, all of which contribute significantly to the Lys content of the endosperm.

The actin cytoskeleton is absolutely required for pollen germination and tube growth, but little is known about the regulation of actin polymer concentrations or dynamics in pollen. Here, we report that latrunculin B (LATB), a potent inhibitor of actin polymerization, had effects on pollen that were distinct from those of cytochalasin D. The equilibrium dissociation constant measured for LATB binding to maize pollen actin was determined to be 74 nM. This high affinity for pollen actin suggested that treatment of pollen with LATB would have marked effects on actin function. Indeed, LATB inhibited maize pollen germination half-maximally at 50 nM, yet it blocked pollen tube growth at one-tenth of that concentration. Low concentrations of LATB also caused partial disruption of the actin cytoskeleton in germinated maize pollen, as visualized by light microscopy and fluorescent-phalloidin staining. The amounts of filamentous actin (F-actin) in pollen were quantified by measuring phalloidin binding sites, a sensitive assay that had not been used previously for plant cells. The amount of F-actin in maize pollen increased slightly upon germination, whereas the total actin protein level did not change. LATB treatment caused a dose-dependent depolymerization of F-actin in populations of maize pollen grains and tubes. Moreover, the same concentrations of LATB caused similar depolymerization in pollen grains before germination and in pollen tubes. These data indicate that the increased sensitivity of pollen tube growth to LATB was not due to general destabilization of the actin cytoskeleton or to decreases in F-actin amounts after germination. We postulate that germination is less sensitive to LATB than tube extension because the presence of a small population of LATB-sensitive actin filaments is critical for maintenance of tip growth but not for germination of pollen, or because germination is less sensitive to partial depolymerization of the actin cytoskeleton.

The actin binding protein profilin has dramatic effects on actin polymerization in vitro and in living cells. Plants have large multigene families encoding profilins, and many cells or tissues can express multiple profilin isoforms. Recently, we characterized several profilin isoforms from maize pollen for their ability to alter cytoarchitecture when microinjected into living plant cells and for their association with poly-L-proline and monomeric actin from maize pollen. In this study, we characterize a new profilin isoform from maize, which has been designated ZmPRO4, that is expressed predominantly in endosperm but is also found at low levels in all tissues examined, including mature and germinated pollen. The affinity of ZmPRO4 for monomeric actin, which was measured by two independent methods, is similar to that of the three profilin isoforms previously identified in pollen. In contrast, the affinity of ZmPRO4 for poly-L-proline is nearly twofold higher than that of native pollen profilin and the other recombinant profilin isoforms. When ZmPRO4 was microinjected into plant cells, the effect on actin-dependent nuclear position was significantly more rapid than that of another pollen profilin isoform, ZmPRO1. A gain-of-function mutant (ZmPRO1-Y6F) was created and found to enhance poly-L-proline binding activity and to disrupt cytoarchitecture as effectively as ZmPRO4. In this study, we demonstrate that profilin isoforms expressed in a single cell can have different effects on actin in living cells and that the poly-L-proline binding function of profilin may have important consequences for the regulation of actin cytoskeletal dynamics in plant cells.

Background The opaque2 mutant is valuable for producing maize varieties with enhanced nutritional value. However, the exact mechanisms by which it improves protein quality and creates a soft endosperm texture are unclear. Given the importance of improving nutritional quality in grain crops, a better understanding of the physiological basis for these traits is necessary. Results In this study, we combined transcript profiling and proteomic analysis to better understand which genes and proteins are altered by opaque2 in the W64A inbred line. These analyses showed that the accumulation of some lysine-rich proteins, such as sorbitol dehydrogenase and glyceraldehyde3-phosphate dehydrogenase, was increased in mature kernels and may contribute substantially to the lysine content of opaque2 endosperm. Some defense proteins such as beta-glucosidase aggregating factor were strongly down regulated and may be regulated directly by opaque2. The mutant also had altered expression of a number of starch biosynthesis genes and this was associated with a more highly crystalline starch. Conclusions The results of these studies revealed specific target genes that can be investigated to further improve nutritional quality and agronomic performance of high lysine maize lines, particularly those based on the presence of the opaque2 mutation. Alteration of amylopectin branching patterns in opaque2 starch could contribute to generation of the soft, starchy endosperm.