The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression

Background  

Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus.     

Mechanistic and Structural Understanding of Uncompetitive Inhibitors of Caspase-6

Inhibition of caspase-6 is a potential therapeutic strategy for some neurodegenerative diseases, but it has been difficult to develop selective inhibitors against caspases. We report the discovery and characterization of a potent inhibitor of caspase-6 that acts by an uncompetitive binding mode that is an unprecedented mechanism of inhibition against this target class. Biochemical assays demonstrate that, while exquisitely selective for caspase-6 over caspase-3 and -7, the compound’s inhibitory activity is also dependent on the amino acid sequence and P1’ character of the peptide substrate. The crystal structure of the ternary complex of caspase-6, substrate-mimetic and an 11 nM inhibitor reveals the molecular basis of inhibition. The general strategy to develop uncompetitive inhibitors together with the unique mechanism described herein provides a rationale for engineering caspase selectivity.     

Localization of PBP3 in Caulobacter crescentus is highly dynamic and largely relies on its functional transpeptidase domain

In rod-shaped bacteria, septal peptidoglycan synthesis involves the late recruitment of the ftsI gene product (PBP3 in Escherichia coli) to the FtsZ ring. We show that in Caulobacter crescentus, PBP3 accumulates at the new pole at the beginning of the cell cycle. Fluorescence recovery after photobleaching experiments reveal that polar PBP3 molecules are, constantly and independently of FtsZ, replaced by those present in the cellular pool, implying that polar PBP3 is not a remnant of the previous division. By the time cell constriction is initiated, all PBP3 polar accumulation has disappeared in favour of an FtsZ-dependent localization near midcell, consistent with PBP3 function in cell division. Kymograph analysis of time-lapse experiments shows that the recruitment of PBP3 to the FtsZ ring is progressive and initiated very early on, shortly after FtsZ ring formation and well before cell constriction starts. Accumulation of PBP3 near midcell is also highly dynamic with a rapid exchange of PBP3 molecules between midcell and cellular pools. Localization of PBP3 at both midcell and pole appears multifactorial, primarily requiring the catalytic site of PBP3. Collectively, our results suggest a role for PBP3 in pole morphogenesis and provide new insights into the process of peptidoglycan assembly during division.     

Conformational constraint in oxazolidinone antibacterials. Part 2: Synthesis and structure-activity studies of oxa-, aza-, and thiabicyclo[3.1.0]hexylphenyl oxazolidinones

A new class of oxazolidinone antibacterials incorporating oxygen-, nitrogen-, or sulfur-containing heterobicyclic C-rings is described. The in vitro potency and in vivo efficacy of these conformationally constrained oxazolidinone analogs are discussed.     

Sub-cellular internalization and organ specific oral delivery of PABA nanoparticles by side chain variation

Background  

Organic nanomaterials having specific biological properties play important roles in in vivo delivery and clearance from the live cells. To develop orally deliverable nanomaterials for different biological applications, we have synthesized several fluorescently labelled, self-assembled PABA nanoparticles using possible acid side chain combinations and tested against insect and human cell lines and in vivo animal model. Flurophores attached to nanostructures help in rapid in vivo screening and tracking through complex tissues. The sub-cellular internalization mechanism of the conjugates was determined. A set of physio-chemical parameters of engineered nanoskeletons were also defined that is critical for preferred uptake in multiple organs of live Drosophila.     

Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli

As one of the final steps in the bacterial growth cycle, daughter cells must be released from one another by cutting the shared peptidoglycan wall that separates them. In Escherichia coli, this delicate operation is performed by several peptidoglycan hydrolases, consisting of multiple amidases, lytic transglycosylases, and endopeptidases. The interactions among these enzymes and the molecular mechanics of how separation occurs without lysis are unknown. We show here that deleting the endopeptidase PBP 4 from strains lacking AmiC produces long chains of unseparated cells, indicating that PBP 4 collaborates with the major peptidoglycan amidases during cell separation. Another endopeptidase, PBP 7, fulfills a secondary role. These functions may be responsible for the contributions of PBPs 4 and 7 to the generation of regular cell shape and the production of normal biofilms. In addition, we find that the E. coli peptidoglycan amidases may have different substrate preferences. When the dd-carboxypeptidase PBP 5 was deleted, thereby producing cells with higher levels of pentapeptides, mutants carrying only AmiC produced a higher percentage of cells in chains, while mutants with active AmiA or AmiB were unaffected. The results suggest that AmiC prefers to remove tetrapeptides from peptidoglycan and that AmiA and AmiB either have no preference or prefer pentapeptides. Muropeptide compositions of the mutants corroborated this latter conclusion. Unexpectedly, amidase mutants lacking PBP 5 grew in long twisted chains instead of straight filaments, indicating that overall septal morphology was also defective in these strains.     

Plant small monomeric G-proteins (RAC/ROPs) of barley are common elements of susceptibility to fungal leaf pathogens,cell expansion and stomata development

Small monomeric RAC/ROP GTPases act as molecular switches in signal transduction processes of plant development and stress responses. They emerged as crucial players in plant-pathogen interactions either by supporting susceptibility or resistance. In a recent publication, we showed that constitutively activated (CA) mutants of different barley (Hordeum vulgare) RAC/ROPs regulate susceptibility to barley fungal leaf pathogens of different life style in a contrasting way. This illustrates the distinctive signalling roles of RAC/ROPs for different plant-pathogen combinations. We also reported the involvement of RAC/ROPs in plant epidermis development in a monocotyledonous plant. Here we further discuss a failure of CA HvRAC/ROP-expressing barley to normally develop stomata.Key words: Hordeum vulgare, G-proteins, RAC, ROP, cell expansion, stomata, transpirationMembers of the RHO family of small G-proteins in plants (RAC/ROPs) regulate signal transduction processes at the plasma membrane.¹ They act as multifunctional signalling switches in plant development and a variety of stress responses. RAC/ROP GTPases play regulatory roles in polar growth and cell morphogenesis in several cell systems including pollen tubes, developing root hairs and leaf pavement cells.²In a recent publication,³ we showed that constitutively activated (CA) mutants of different barley (Hordeum vulgare) RAC/ROPs support susceptibility to the barley powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh). CA HvRAC1 supported susceptibility to biotrophic Bgh but resistance to hemibiotrophic Magnaporthe oryzae in barley at the penetration level in both cases. Additionally, CA HvRAC1 supported local callose deposition at sites of attack from Bgh and a secondary H₂O₂ burst in whole non-penetrated epidermal cells. This supports a regulatory function of RAC/ROPs in plant defence¹ and the potential corruption of defence pathways in susceptibility to Bgh. Because the rice ortholog of HvRAC1, OsRAC1, can regulate an H₂O₂ burst via activation of the plasma membrane NADPH oxidase OsRBOHB,⁴ one can speculate that the secondary H₂O₂ burst in CA HvRAC1 barley could also be caused by over-activation of an NADPH oxidase. However, CA HvRAC1 barley was also more susceptible to fungal penetration, and penetrated cells did not show an H₂O₂ burst. Hence, CA HvRAC1 did not contribute to penetration resistance, and the H₂O₂ burst might have been suppressed by Bgh after successful penetration. Interestingly, Bgh secretes a catalase during interaction with the plant.⁵The involvement of RAC/ROPs in plant development has been widely studied in the dicots Arabidopsis and tobacco. In Arabidopsis, CA AtRAC/ROPs disturb root hair tip growth and epidermal cell morphogenesis.^6,7 We showed similar developmental aberrations as a result of CA HvRAC/ROP expression in monocotyledonous barley. Root hair polarity disruption and enhanced leaf epidermal cell expansion was observed in CA HvRAC/ROP expressing barley. Here, we further report on reduced or abnormal development of stomata as an effect of CA HvRAC/ROP expression.In barley, stomata and short epidermal cells alternate in a row of leaf epidermal cells (Fig. 1A). The number of stomata number was significantly reduced in three CA HvRAC/ROP (CA HvRACB, CAHvRAC3, CA HvRAC1) expressing barley genotypes when compared to azygous controls (barley siblings that lost the transgene due to segregation) (Fig. 1E). In part, this could be explained by enhanced length of epidermal cells intercalated between stomata (Fig. 1B). The presence of longer epidermal cells in all CA HvRAC/ROP-barleys further supports that RAC/ROPs are operating in epidermal cell expansion.³Open in a separate windowFigure 1Stomatal abnormalities observed in CA HvROPexpressing transgenic barley leaves. (A) Wild type leaf adaxial epidermis with alternating stomata complexes (arrows) and short epidermal cells (asterisk). (B) Presence of more than one short epidermal cell in between two stomata. Arrows point the stomata. Double headed arrows highlight intercalated cells with enhanced cell length (C) Two stomata lacking an intercalated short epidermal cell. (D) Stoma failed to develop and left an abnormal blank cell. (E) Average number of stomata present in 5 cm of a stomatal row in transgenic plants expressing distinct CA barley CA HvRAC/ROPs. For all samples, stomatal rows present on either side of the mid rib were counted in the leaf upper epidermis. Fully expanded leaves of 3-weeks-old barley plants were used for counting stomata. Error bars show 95% confidence intervals. Repetition of the experiment led to similar results. Scale bars = 50 µm.Previously, we carried out porometry experiments to measure stomata conductivity in CA HvRACB expressing barley leaves.⁸ The CA HvRACB leaves showed up to 50% less transpiration than azygous controls without any treatment. Additionally, CA HvRACB leaves were less responsive to abscisic acid (ABA) and subsequently they could not effectively reduce transpiration when treated with ABA or when cut-off from water supply.⁸ Our data on numbers of stomata per leaf segment could now explain the lower rates of transpiration in non-stressed CA HvRACB barley when compared to wild type.Apart from the stomata number, developmental abnormalities were observed in the arrangement of epidermal cells. Generally, the shape of epidermal cells was less regular in CA HvRAC/ROP barley.³ We also observed the presence of more than one short epidermal cell in between two stomata (Fig. 1B) or two stomata lacking an intercalated short epidermal cell (Fig. 1C), or stomata failed to develop, which ended up in an abnormally short epidermal cell (Fig. 1D). Although such abnormalities were also rarely observed in wild type plants, all three CA HvRAC/ROP-barley leaves exhibited a clearly higher frequency of abnormalities in a given length of a stomata row. Together, CA HvRAC/ROPs had an effect on both the number and development of stomata. These observations suggest that RAC/ROPs are not only operating in cell expansion but also in barley cell differentiation for stomata development.