Alan Cookson

Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes

Despite the economic importance of grasses as food, feed, and energy crops, little is known about the genes that control their cell wall synthesis, assembly, and remodelling. Here a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis is provided. Differential gene expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material. This is one of only a few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall biogenesis in grasses. The results suggest that many proteins involved in cell wall processes during normal development are also recruited during defence-related cell wall remodelling events. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in cell wall-related processes, increasing our knowledge of cell wall biogenesis and its regulation in grasses. Since several grasses are currently being developed as lignocellulosic feedstocks for biofuel production, this improved understanding of grass cell wall biogenesis is timely, as it will facilitate the manipulation of traits favourable for sustainable food and biofuel production.

Predatory activity of Myxococcus xanthus outer-membrane vesicles and properties of their hydrolase cargo

The deltaproteobacterium Myxococcus xanthus predates upon members of the soil microbial community by secreting digestive factors and lysing prey cells. Like other Gram-negative bacteria, M. xanthus produces outer membrane vesicles (OMVs), and we show here that M. xanthus OMVs are able to kill Escherichia coli cells. The OMVs of M. xanthus were found to contain active proteases, phosphatases, other hydrolases and secondary metabolites. Alkaline phosphatase activity was found to be almost exclusively associated with OMVs, implying that there is active targeting of phosphatases into OMVs, while other OMV components appear to be packaged passively. The kinetic properties of OMV alkaline phosphatase suggest that there may have been evolutionary adaptation of OMV enzymes to a relatively indiscriminate mode of action, consistent with a role in predation. In addition, the observed regulation of production, and fragility of OMV activity, may protect OMV-producing cells from exploitation by M. xanthus cheating genotypes and/or other competitors. Killing of E. coli by M. xanthus OMVs was enhanced by the addition of a fusogenic enzyme (glyceraldehyde-3-phosphate dehydrogenase; GAPDH), which triggers fusion of vesicles with target membranes within eukaryotic cells. This suggests that the mechanism of prey killing involves OMV fusion with the E. coli outer membrane. M. xanthus secretes GAPDH, which could potentially modulate the fusion of co-secreted OMVs with prey organisms in nature, enhancing their predatory activity.

Flowering induction in the bioenergy grass Miscanthus sacchariflorus is a quantitative short-day response, whilst delayed flowering under long days increases biomass accumulation

Miscanthus sacchariflorus is a fast-growing C4 perennial grass that can naturally hybridize with M. sinensis to produce interspecific hybrids, such as the sterile triploid M.× giganteus. The creation of such hybrids is essential for the rapid domestication of this novel bioenergy crop. However, progress has been hindered by poor understanding of the environmental cues promoting floral transition in M. sacchariflorus, which flowers less readily than M. sinensis. The purpose of this work was to identify the flowering requirements of M. sacchariflorus genotypes in order to expedite the introduction of new germplasm optimized to different environments. Six M. sacchariflorus accessions collected from a range of latitudes were grown under controlled photoperiod and temperature conditions, and flowering, biomass, and morphological phenotypic data were captured. Results indicated that M. sacchariflorus, irrespective of origin, is a quantitative short-day plant. Flowering under static long days (15.3h daylength), compared with shorter photoperiods, was delayed by an average 61 d, with an average associated increase of 52% of above-ground biomass (DM plant–1). Timing of floral initiation occurred between photoperiods of 14.2h and 12.1h, and accumulated temperatures of 553–1157 °C above a base temperature of 10 °C. Miscanthus sacchariflorus flowering phenology closely resembles that of Sorghum and Saccharum, indicating potentially similar floral pathways and suggesting that determination of the underlying genetic mechanisms will be facilitated by the syntenic relationships existing between these important C4 grasses.

Starch metabolism in the fructan-grasses: Patterns of starch accumulation in excised leaves of Lolium temulentum L.

Summary Excised and illuminated leaves of temperate gramineae have previously provided a powerful system for the analysis of the regulation of partitioning of photosynthate between sucrose and fructan. This paper complements previous data by describing the concomitant accumulation of transitory starch, an assimilate which has been ignored in this system. Leaves of Lolium temulentum were depleted to near-zero reserve carbohydrate content. In this condition, the tissue contained no detectable fructan or starch and only a trace of sucrose. When subsequently excised and illuminated continuously, the accumulation of sucrose and starch commenced immediately and occurred simultaneously. Starch anabolism was constitutive and the polymer was apparently synthesised de novo . The maximal rate of starch accumulation, at 0.6 mg g −1 fresh mass, was 5-10-fold lower than that of sucrose. Fructan was also synthesised de novo and was induced after a lag of 8 h, after which rates of net sucrose and starch accumulation slowed, ceasing completely by 14-16 h. Whilst total non-structural carbohydrate concentration increased continuously, reaching 56 mg g −1 at 30 h, starch concentration was asymptotic and was limited to a maximum of only 7 mg g −1 reached at 14-16 h. Hence, net starch accumulation was not restricted by the continued production of photosynthate. The illumination period spanned 1.25 diurnal cycles. Despite continued photoassimilation, there was no resumption of net starch synthesis at the beginning of the second cycle and hence the limitation of net starch accumulation was not imposed by an endogenous circadian rhythmicity. When assimilate partitioning into fructan was abolished by transpirational feeding of cycloheximide, sucrose concentration increased 2.7-fold to 49 mg g −1 . This abnormally high concentration did not feedback to enhance starch accumulation. Transpirational feeding of 10 mmol/L mannose inhibited sucrose accumulation by c .90 %, but this inhibition was not accompanied by an increase net starch accumulation, rather, starch accumulation was inhibited by 60 %. Mannose caused the formation of maltose in the tissue. Starch synthesis, in common with sucrose and fructan syntheses, was shown to be localised predominantly in mesophyll cells where presumably the control of partitioning between these three assimilates is exercised. The low rates, restricted tissue concentration, sucrose-insensitivity and mannose-inhibition of starch synthesis differ from many species where starch is the primary reserve. Although the available information is limited, some of these features are in common with other fructan grasses. The low capacity for starch accumulation provides a possible explanation for the evolution of fructan synthesis in these species.

Rumen protozoa are rich in polyunsaturated fatty acids due to the ingestion of chloroplasts

Within this study, we investigated whether the polyunsaturated fatty acids (PUFA)-rich nature of rumen protozoa is a consequence of ingestion of PUFA-rich chloroplasts. Four Hereford x Friesian steers were offered hay [low 18:3 (n-3) and low chlorophyll concentration] followed by freshly cut perennial ryegrass [high 18:3 (n-3) and high chlorophyll concentration] for 16 days. On the 14th and 16th days, rumen protozoa as well as attached and planktonic bacteria were fractionated 1 h before (-1 h), 2 and 6 h postfeeding, and their fatty acid concentrations determined. Protozoa fractionated from fresh grass-fed steers were richer (P<0.05) in PUFA, except conjugated linoleic acid, for all time points compared with those from hay-fed steers. Protozoal density was higher (P<0.05) for grass compared with hay. Entodinomorphid abundance was 3.4 times higher on fresh grass (P<0.01) compared with hay. Confocal microscopy and transmission electron microscopy confirmed that Epidinium spp. were commonly saturated with intracellular cytoplasmic chloroplasts. These data suggest that engulfment of chloroplasts is a major contributor to the high 18:3 (n-3) concentration of protozoa.

Endophytic bacteria in Miscanthus seed : Implications for germination, vertical inheritance of endophytes, plant evolution, and breeding

With growing interest in the role of microbiomes, and symbionts in particular, the aim of this study was to determine the diversity of the bacterial endophyte population within Miscanthus and to ascertain the extent of vertical transmission via the seed. A great diversity of endophytic bacteria was found in all parts of the mature plant (rhizome, root, stem and leaf), and in seedlings grown from sterilized seed grown in sterile conditions. A total of three phyla and five families of bacteria were identified as cultures compared to 19 phyla and 85 families using 16S rDNA amplification and sequencing. Not all cultured bacteria could be identified by 16S rDNA, implying that the true diversity is even greater. More bacterial diversity was identified in sterile‐grown seedlings than in all parts of the mature plant combined, 17 and 13 phyla, respectively, with 11 in common. Five phyla were present in all plant samples examined. Vertical transmission via the seed may therefore be a major source of endophytes in Miscanthus, presumably supplemented by ingress of soil bacteria as the plant grows. Bacteria identified from the mature plant were predominantly similar to known bacterial sequences in GenBank, but a small number from the stem and many from the seed were novel, potentially adapted to an in planta life cycle. Endophytic bacteria were found to form spores and other dense structures, and this provides a mechanism for long‐term survival and seed transmission. The staining of germinating seeds identified bacteria at the root tip of the emerging radicle. We propose that seed transmission of bacterial endophytes requires adaptation of both plant and microbes, plays a role in germination and has evolutionary significance and implications for future plant breeding approaches, in Miscanthus and more widely.

Gene expression patterns, localization, and substrates of polyphenol oxidase in red clover ( Trifolium pratense L.).

Polyphenol oxidase (PPO) genes and their corresponding enzyme activities occur in many plants; natural PPO substrates and enzyme/substrate localization are less well characterized. Leaf and root PPO activities in Arabidopsis and five legumes were compared with those of high-PPO red clover ( Trifolium pratense L.). Red clover PPO enzyme activity decreased leaves > stem > nodules > peduncle = petiole > embryo; PPO1 and PPO4 genes were expressed early in leaf emergence, whereas PPO4 and PPO5 predominated in mature leaves. PPO1 was expressed in embryos and nodules. PPO substrates, phaselic acid and clovamide, were detected in leaves, and clovamide was detected in nodules. Phaselic acid and clovamide, along with caffeic and chlorogenic acids, were suitable substrates for PPO1, PPO4, and PPO5 genes expressed in alfalfa ( Medicago sativa L.) leaves. PPO enzyme presence and activity were colocalized in leaves and nodules by cytochemistry. Substrates and PPO activity were localized in developing squashed cell layer of nodules, suggesting PPO may have a developmental role in nodules.

Potential sources of high value chemicals from leaves, stems and flowers of Miscanthus sinensis ‘Goliath’ and Miscanthus sacchariflorus

Society demands chemicals from sustainable sources. Identification of commercially important chemicals in crops increases value in biorefineries and reduces reliance on petrochemicals. Miscanthus sinensis and Miscanthus sacchariflorus are high-yielding distinct plants, which are sources of high-value chemicals and bioethanol through fermentation. Cinnamates in leaves, stems and flowers were analysed by LC-ESI-MS(n). Free phenols were extracted and separated chromatographically. More than twenty hydroxycinnamates were identified by UV and LC-ESI-MS(n). Several cinnamate hexosides were detected in the M. sinensis flower and in M. sacchariflorus (leaf and stem). Hydroxybenzoic acids and their hexosides were observed in leaf and stem of M. sacchariflorus. Higher concentrations of 3-feruloylquinic acid were observed in M. sacchariflorus stem, suggesting a role in cell-wall biosynthesis. This technique can be used to screen plants in a mapping family to identify genotypes/species with high concentrations of phenols. Plants with low concentrations of antimicrobial phenols may be good feedstocks for fermentation.

Polyphenol oxidase affects normal nodule development in red clover (Trifolium pratense L.)

Polyphenol oxidase (PPO) may have multiple functions in tissues depending on its cellular or tissue localization. Here we use PPO RNAi transformants of red clover (Trifolium pratense) to determine the role PPO plays in normal development of plants, and especially in N2-fixing nodules. In red clover, PPO was not essential for either growth or nodule production, or for nodule function in plants grown under optimal, N-free conditions. However, absence of PPO resulted in a more reduced environment in all tissues, as measured by redox potential, and caused subtle developmental changes in nodules. Leaves and, to a lesser extent nodules, lacking PPO tended to accumulate phenolic compounds. A comparison of nodules of two representative contrasting clones by microscopy revealed that nodules lacking PPO were morphologically and anatomically subtly altered, and that phenolics accumulated in different cells and tissues. Developing nodules lacking PPO were longer, and there were more cell layers within the squashed cell layer (SCL), but the walls of these cells were less thickened and the cells were less squashed. Within the N2-fixing zone, bacteroids appeared more granular and were less tightly packed together, and were similar to developmentally compromised bacteroids elicited by catalase mutant rhizobia reported elsewhere.

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.Antibiotics: Potential in the rumenAnti-microbial molecules made by microbes in the gut of ruminant animals could become new weapons against antibiotic-resistant infections. An international team of researchers led by Sharon Huws at Queen’s University Belfast, UK, identified three anti-microbial peptides in the rumen of animals such as cattle, sheep and goats. The peptides—short proteins—were highly active in laboratory trials against several clinically important drug-resistant infections. These included methicillin resistant Staphylococcus aureus (MRSA), a notorious cause of life-threatening infections, especially in patients with weakened immunity. There is growing interest in using peptides as alternatives to existing antibiotics. The findings, initiated by examining a ‘library’ of molecular data, suggest that the rumen is an under-explored resource that may harbor many medically useful antimicrobials. The possibilities should be investigated further, with promising molecules being tested in clinical conditions.