Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII_170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.     

SALT-OVERLY SENSITIVE5 Mediates Arabidopsis Seed Coat Mucilage Adherence and Organization through Pectins

Interactions between cell wall polymers are critical for establishing cell wall integrity and cell-cell adhesion. Here, we exploit the Arabidopsis (Arabidopsis thaliana) seed coat mucilage system to examine cell wall polymer interactions. On hydration, seeds release an adherent mucilage layer strongly attached to the seed in addition to a nonadherent layer that can be removed by gentle agitation. Rhamnogalacturonan I (RG I) is the primary component of adherent mucilage, with homogalacturonan, cellulose, and xyloglucan constituting minor components. Adherent mucilage contains rays composed of cellulose and pectin that extend above the center of each epidermal cell. CELLULOSE SYNTHASE5 (CESA5) and the arabinogalactan protein SALT-OVERLY SENSITIVE5 (SOS5) are required for mucilage adherence through unknown mechanisms. SOS5 has been suggested to mediate adherence by influencing cellulose biosynthesis. We, therefore, investigated the relationship between SOS5 and CESA5. cesa5-1 seeds show reduced cellulose, RG I, and ray size in adherent mucilage. In contrast, sos5-2 seeds have wild-type levels of cellulose but completely lack adherent RG I and rays. Thus, relative to each other, cesa5-1 has a greater effect on cellulose, whereas sos5-2 mainly affects pectin. The double mutant cesa5-1 sos5-2 has a much more severe loss of mucilage adherence, suggesting that SOS5 and CESA5 function independently. Double-mutant analyses with mutations in MUCILAGE MODIFIED2 and FLYING SAUCER1 that reduce mucilage release through pectin modification suggest that only SOS5 influences pectin-mediated adherence. Together, these findings suggest that SOS5 mediates adherence through pectins and does so independently of but in concert with cellulose synthesized by CESA5.Cellulosic cell walls are a defining feature of land plants. Primary cell walls are composed of three major classes of polysaccharides: cellulose, hemicelluloses, and pectins. In addition, approximately 10% of the primary cell wall is composed of protein (Burton et al., 2010). Cell walls provide mechanical support for the cell, and cell wall carbohydrates in the middle lamellae mediate cell-cell adhesion (Caffall and Mohnen, 2009). Current models of cell wall structure depict a cellulose-hemicellulose network embedded in an independent pectin gel (for review, see Albersheim et al., 2011). These components are believed to interact through both covalent and noncovalent bonds to provide structure and strength to the cell wall, although the relative importance of pectin and its interactions with the hemicellulose-cellulose network remain unclear (for review, see Cosgrove, 2005).Another gap in our understanding of cell wall structure and assembly is the role of arabinogalactan proteins (AGPs). AGPs are a family of evolutionarily conserved secreted proteins highly glycosylated with type II arabinogalactans, and they can be localized to the plasma membrane by a C-terminal glycophosphatidylinositol (GPI) lipid anchor (for review, see Schultz et al., 2000; Showalter, 2001; Johnson et al., 2003; Seifert and Roberts, 2007; Ellis et al., 2010). AGPs can be extensively modified in the cell wall; many glycosyl hydrolases can affect AGP function by cleaving their glycosyl side chains (Sekimata et al., 1989; Cheung et al., 1995; Wu et al., 1995; Kotake et al., 2005). The GPI anchor can also be cleaved, releasing the AGPs from the membrane into the cell wall (Schultz et al., 2000). Although their exact roles are still unclear, AGPs have been proposed to interact with cell wall polysaccharides, initiate intracellular signaling cascades, and influence a wide variety of biological processes (for review, see Seifert and Roberts, 2007; Ellis et al., 2010; Tan et al., 2013).Many fasciclin-like AGPs (FLAs), which contain at least one fasciclin domain (FAS) associated with protein-protein interactions, have been suggested to influence cellulose biosynthesis or organization (Seifert and Roberts, 2007; Li et al., 2010; MacMillan et al., 2010). FLA3 RNA interference lines have reduced intine cell wall biosynthesis and loss of Calcofluor white (a fluorescent dye specific for glycan molecules) staining in aborted pollen grains (Li et al., 2010). A fla11 fla12 double mutant was shown to have reduced cellulose deposition, altered cellulose microfibril angle, and reduced cell wall integrity (MacMillan et al., 2010). The fla11 fla12 double mutant also had reductions in arabinans, galactans, and rhamnose (MacMillan et al., 2010). FLA4/SALT-OVERLY SENSITIVE5 (SOS5) was identified in a screen for salt sensitivity in roots. The SOS5 gene encodes an FLA protein with a GPI anchor, two AGP-like domains, and two FAS domains (Shi et al., 2003). Plants homozygous for the loss-of-function conditional allele sos5-1 have thinner root cell walls that appear less organized (Shi et al., 2003). The presence of the two FAS domains has led to the suggestion that SOS5 may interact with other proteins, forming a network that strengthens the cell wall (Shi et al., 2003). SOS5 is involved in regulation of cell wall rheology through a pathway involving two Leu-rich repeat receptor-like kinases, FEI1 and FEI2 (Xu et al., 2008). SOS5 and FEI2 are also required for normal seed coat mucilage adherence and hypothesized to do so by influencing cellulose biosynthesis (Harpaz-Saad et al., 2011, 2012).Arabidopsis (Arabidopsis thaliana) seed coat mucilage is a powerful model for studying cell wall biosynthesis and polysaccharide interactions (Arsovski et al., 2010; Haughn and Western, 2012). Seed coat epidermal cells sequentially produce two distinct types of secondary cell walls with unique morphologies and properties (Western et al., 2000; Windsor et al., 2000). Between approximately 5 and 9 d approximate time of fertilization (DPA), seed coat epidermal cells synthesize mucilage and deposit it in the apoplast, creating a donut-shaped mucilage pocket that surrounds a central cytoplasmic column (Western et al., 2000, 2004; Haughn and Chaudhury, 2005). From 9 to 13 DPA, the cytoplasmic column is gradually replaced by a cellulose-rich, volcano-shaped secondary cell wall called the columella (Beeckman et al., 2000; Western et al., 2000; Windsor et al., 2000; Stork et al., 2010; Mendu et al., 2011).Seed mucilage is composed primarily of relatively unbranched rhamnogalacturonan I (RG I) with minor amounts of homogalacturonan (HG), cellulose, and hemicelluloses (for review, see Haughn and Western, 2012). When mucilage is hydrated, it expands rapidly from the apoplastic pocket, forming a halo that surrounds the seed. Mucilage separates into two fractions: a loose nonadherent fraction and an inner adherent fraction that can only be released by vigorous shaking, strong bases, or glycosidases (for review, see North et al., 2014). Galactans and arabinans are also present in mucilage, and their regulation by glycosidases is required for correct mucilage hydration (Dean et al., 2007; Macquet et al., 2007b; Arsovski et al., 2009). For example, β-XYLOSIDASE1 encodes a bifunctional β-d-xylosidase/α-l-arabinofuranosidase required for arabinan modification in mucilage, and β-xylosidase1 mutant seeds have a delayed mucilage release phenotype (Arsovski et al., 2009). MUCILAGE MODIFIED2 (MUM2) encodes a β-d-galactosidase, and mum2 seeds fail to release mucilage when hydrated in water (Dean et al., 2007; Macquet et al., 2007b). MUM2 is believed to modify RG I galactan side chains but may also affect the galactan component of other mucilage components (Dean et al., 2007; Macquet et al., 2007b). Galactans are capable of binding to cellulose in vitro and could affect mucilage hydration through pectin-cellulose interactions (Zykwinska et al., 2005, 2007a, 2007b; Dick-Pérez et al., 2011; Wang et al., 2012), although carbohydrate linkage analysis suggests that the galactan side chains are very short.Several studies indicate that seed mucilage extrusion and expansion are also influenced by methylesterification of HG. For example, both SUBTILISIN-LIKE SER PROTEASE1.7 and PECTIN METHYLESTERASE INHIBITOR6 are required for proper methyl esterification of mucilage (Rautengarten et al., 2008; Saez-Aguayo et al., 2013). Mutations in another gene, FLYING SAUCER1 (FLY1; a transmembrane E3 ubiquitin ligase), reduce the degree of pectin methylesterification in mucilage and cause increased mucilage adherence and defective mucilage extrusion (Voiniciuc et al., 2013). fly1 seeds have disc-like structures at the edge of the mucilage halo, which are outer primary cell wall fragments that detach from the columella during extrusion and are difficult to separate from the adherent mucilage (Voiniciuc et al., 2013).Recently, CELLULOSE SYNTHASE5 (CESA5) and SOS5 were proposed to facilitate cellulose-mediated mucilage adherence (Harpaz-Saad et al., 2011; Mendu et al., 2011; Sullivan et al., 2011). A simple hypothesis for the role of CESA5 in mucilage adherence is that it synthesizes cellulose, which interacts with the mucilage pectin to mediate adherence. Loss of CESA5 function results in a reduction of mucilage cellulose biosynthesis and a less adherent mucilage cell wall matrix (Mendu et al., 2011; Sullivan et al., 2011). The role of SOS5 in mucilage adherence is more difficult to explain. SOS5 null mutations cause a loss-of-adherence phenotype similar to cesa5-1 seeds, suggesting that SOS5 may regulate mucilage adherence by influencing CESA5 function (Harpaz-Saad et al., 2011). However, the mechanism through which SOS5 could influence CESA5 and/or cellulose biosynthesis is not clear.To better understand the role of SOS5 in mucilage adherence and its relationship to CESA5, we thoroughly investigated the seed coat epidermal cell phenotypes of the cesa5-1 and sos5-2 single mutants as well as those of the cesa5-1 sos5-2 double mutant. We also investigated how cellulose, SOS5, and pectin interact to mediate mucilage adherence by constructing double mutants with either cesa5-1 or sos5-2 together with either mum2-1 or fly1. Our results suggest that SOS5 mediates mucilage adherence independently of CESA5. Furthermore, compared with CESA5, SOS5 has a greater influence on mucilage pectin structure, suggesting that SOS5 mediates mucilage adherence through pectins, not cellulose.     

Structural and biochemical characterization of ZhuI aromatase/cyclase from the R1128 polyketide pathway

Aromatic polyketides comprise an important class of natural products that possess a wide range of biological activities. The cyclization of the polyketide chain is a critical control point in the biosynthesis of aromatic polyketides. The aromatase/cyclases (ARO/CYCs) are an important component of the type II polyketide synthase (PKS) and help fold the polyketide for regiospecific cyclizations of the first ring and/or aromatization, promoting two commonly observed first-ring cyclization patterns for the bacterial type II PKSs: C7-C12 and C9-C14. We had previously reported the crystal structure and enzymological analyses of the TcmN ARO/CYC, which promotes C9-C14 first-ring cyclization. However, how C7-C12 first-ring cyclization is controlled remains unresolved. In this work, we present the 2.4 ? crystal structure of ZhuI, a C7-C12-specific first-ring ARO/CYC from the type II PKS pathway responsible for the production of the R1128 polyketides. Though ZhuI possesses a helix-grip fold shared by TcmN ARO/CYC, there are substantial differences in overall structure and pocket residue composition that may be important for directing C7-C12 (rather than C9-C14) cyclization. Docking studies and site-directed mutagenesis coupled to an in vitro activity assay demonstrate that ZhuI pocket residues R66, H109, and D146 are important for enzyme function. The ZhuI crystal structure helps visualize the structure and putative dehydratase function of the didomain ARO/CYCs from KR-containing type II PKSs. The sequence-structure-function analysis described for ZhuI elucidates the molecular mechanisms that control C7-C12 first-ring polyketide cyclization and builds a foundation for future endeavors into directing cyclization patterns for engineered biosynthesis of aromatic polyketides.     

Ni-Enhanced Charge Transport via π-π Stacking Corridor in Metallic DNA

The mechanism underlying DNA charge transport is intriguing. However, poor conductivity of DNA makes it difficult to detect DNA charge transport. Metallic DNA (M-DNA) has better conducting properties than native DNA. Ni²⁺ may chelate in DNA and thus enhance DNA conductivity. On the basis of this finding, it is possible to reveal the mechanisms underlying DNA charge transport. The conductivity of various Ni-DNA species such as single-stranded, full complement, or mismatched sequence molecules was systematically tested with ultraviolet absorption and electrical or chemical methods. The results showed that the conductivity of single-stranded Ni-DNA (Ni-ssDNA) was similar to that of a native DNA duplex. Moreover, the resistance of Ni-DNA with a single basepair mismatch was significantly higher than that of fully complementary Ni-DNA duplexes. The resistance also increased exponentially as the number of mismatched basepairs increased linearly after the tunneling current behavior predicted by the Simmons model. In conclusion, the charges in Ni²⁺-doped DNA are transported through the Ni²⁺-mediated π−π stacking corridor. Furthermore, Ni-DNA acts as a conducting wire and exhibits a tunneling barrier when basepair mismatches occur. This property may be useful in detecting single basepair mismatches.     

Aurora-A phosphorylates Augmin complex component Hice1 protein at an N-terminal serine/threonine cluster to modulate its microtubule binding activity during spindle assembly

Proper assembly of mitotic spindles requires Hice1, a spindle-associated protein. Hice1 possesses direct microtubule binding activity at its N-terminal region and contributes to intraspindle microtubule nucleation as a subunit of the Augmin complex. However, whether microtubule binding activity of Hice1 is modulated by mitotic regulators remains unexplored. Here, we found that Aurora-A kinase, a major mitotic kinase, specifically binds to and phosphorylates Hice1. We identified four serine/threonine clusters on Hice1 that can be phosphorylated by Aurora-A in vitro. Of the four clusters, the Ser/Thr-17-21 cluster was the most critical for bipolar spindle assembly, whereas other phospho-deficient point mutants had a minimal effect on spindle assembly. Immunostaining with a phospho-Ser-19/20 phospho-specific antibody revealed that phosphorylated Hice1 primarily localizes to spindle poles during prophase to metaphase but gradually diminishes after anaphase. Consistently, the phospho-mimic 17-21E mutant reduced microtubule binding activity in vitro and diminished localization to spindles in vivo. Furthermore, expression of the 17-21E mutant led to decreased association of Fam29a, an Augmin component, with spindles. On the other hand, expression of the phospho-deficient 17-21A mutant permitted intraspindle nucleation but delayed the separation of early mitotic spindle poles and the timely mitotic progression. Taken together, these results suggest that Aurora-A modulates the microtubule binding activity of Hice1 in a spatiotemporal manner for proper bipolar spindle assembly.     

An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

Klebsiella pneumoniae is a Gram-negative bacterium of the family Enterobacteriaceae that possesses diverse metabolic capabilities: many strains are leading causes of hospital-acquired infections that are often refractory to multiple antibiotics, yet other strains are metabolically engineered and used for production of commercially valuable chemicals. To study its metabolism, we constructed a genome-scale metabolic model (iYL1228) for strain MGH 78578, experimentally determined its biomass composition, experimentally determined its ability to grow on a broad range of carbon, nitrogen, phosphorus and sulfur sources, and assessed the ability of the model to accurately simulate growth versus no growth on these substrates. The model contains 1,228 genes encoding 1,188 enzymes that catalyze 1,970 reactions and accurately simulates growth on 84% of the substrates tested. Furthermore, quantitative comparison of growth rates between the model and experimental data for nine of the substrates also showed good agreement. The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism.     

Epithelial cell adhesion molecule (EpCAM) complex proteins promote transcription factor-mediated pluripotency reprogramming

Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein that is highly expressed in embryonic stem cells (ESCs) and its role in maintenance of pluripotency has been suggested previously. In epithelial cancer cells, activation of the EpCAM surface-to-nucleus signaling transduction pathway involves a number of membrane proteins. However, their role in somatic cell reprogramming is still unknown. Here we demonstrate that EpCAM and its associated protein, Cldn7, play a critical role in reprogramming. Quantitative RT-PCR analysis of Oct4, Sox2, Klf4, and c-Myc (OSKM) infected mouse embryonic fibroblasts (MEFs) indicated that EpCAM and Cldn7 were up-regulated during reprogramming. Analysis of numbers of alkaline phosphatase- and Nanog-positive clones, and the expression level of pluripotency-related genes demonstrated that inhibition of either EpCAM or Cldn7 expression resulted in impairment in reprogramming efficiency, whereas overexpression of EpCAM, EpCAM plus Cldn7, or EpCAM intercellular domain (EpICD) significantly enhanced reprogramming efficiency in MEFs. Furthermore, overexpression of EpCAM or EpICD significantly repressed the expression of p53 and p21 in the reprogramming MEFs, and both EpCAM and EpICD activated the promoter activity of Oct4. These observations suggest that EpCAM signaling may enhance reprogramming through up-regulation of Oct4 and possible suppression of the p53-p21 pathway. In vitro and in vivo characterization indicated that the EpCAM-reprogrammed iPSCs exhibited similar molecular and functional features to the mouse ESCs. In summary, our studies provide additional insight into the molecular mechanisms of reprogramming and suggest a more effective means of induced pluripotent stem cell generation.