How to Review a Manuscript, from MBoC

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A 2011 editorial from the journal Molecular Biology of the Cell (MBoC).

Any jackass can trash a manuscript, but it takes good scholarship to create one (how MBoC promotes civil and constructive peer review)

http://www.molbiolcell.org/content/22/5/525.long

Key points:

  1. Review a manuscript only if you can do so objectively
  2. Review a manuscript only if you can do so in a timely manner
  3. Understand your role
  4. Recognize the authors’ efforts and the merits of the work while being clear in identifying faults
  5. Be critical, but be constructive
  6. Be judicious in suggesting additional work
  7. Leave it to future generations to judge a manuscript’s impact
  8. Be a champion for your field
  9. Remember that it is not your paper
  10. Be a good role model

Chinese plant science and Journal of Experimental Botany

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This week’s post was written by Jonathan Ingram, Senior Commissioning Editor / Science Writer for the Journal of Experimental Botany. Jonathan moved from lab research into publishing and communications with the launch of Trends in Plant Science in 1995, then going on to New Phytologist and, in the third sector, Age UK and Mind.

 

In this week of the XIXth International Botanical Congress (IBC) in Shenzhen, it seems appropriate to highlight outstanding research from labs in China. More than a third of the current issue of Journal of Experimental Botany is devoted to papers from labs across this powerhouse of early 21st century plant science.

 

Collaborations are key, and this was a theme that came up time again at the congress. The work by Yongzhe Gu et al. is a fine example, involving scientists at four institutions studying a WRKY gene in wild and cultivated soybean: in Beijing, the State Key Laboratory of Systematic and Evolutionary Botany at the Institute of Botany in the Chinese Academy of Sciences, and the University of the Chinese Academy of Sciences; and in Harbin (Heilongjiang), the Crop Tillage and Cultivation Institute at Heilongjiang Academy of Agricultural Sciences, and the College of Agriculture at Northeast Agricultural University. Interest here centers on the changes which led to the increased seed size in cultivated soybean with possible practical application in cultivation and genetic improvement of such a vital crop.

 

Read the full post on the Global Plant Council blog.

Auxin Biosynthesis and Wheat Yield

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In plants, there are two biosynthetic pathways for the production of the plant hormone indole-3-acetic acid (IAA), namely the Trp-dependent and the Trp-independent pathways. Shao et al. (10.1104/pp.17.00094) have performed a genome-wide analysis to identify a key gene in wheat that functions in the tryptophan-dependent pathway of IAA biosynthesis, namely Tryptophan Aminotransferase of Arabidopsis1/Tryptophan Aminotransferase-Related (TAA1/TAR).

TAR converts Trp to indole-3-pyruvic acid, an intermediate that is then converted by other enzymes to form IAA. Unlike other IAA biosynthesis genes, the overexpression of TAA1/TAR genes does not result in growth defects.   By sequence mining together with gene cloning, the authors have identified 15 TaTAR genes in wheat. TaTAR2.1 had the most abundant transcripts among the TaTAR2 genes and was expressed mainly in roots and up-regulated by low nitrogen (N) availability. Knockdown of TaTAR2.1 caused vegetative and reproductive deficiencies and impaired lateral root growth under both high- and low-N conditions. Overexpressing TaTAR2.1-3A in wheat enhanced lateral root branching, plant height, spike number, grain yield, and aerial N accumulation under different N supply levels. In addition, overexpressing TaTAR2.1-3A in Arabidopsis elevated the accumulation of IAA in the primary root tip, lateral root tip, lateral root primordia, cotyledon and hypocotyl. Overexpression of TaTAR2.1-3A   also led to an increase in primary root length, lateral root number, and shoot fresh weight under high- and low-N conditions. These results suggest that TaTAR2.1 is critical for wheat growth and also shows potential for genetic engineering with the goal of improving the grain yield of wheat.

A MicroRNA Switch that Controls Lateral Root Growth and Nodulation

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Legume roots form two types of organs, lateral roots and symbiotic nodules, which participate, respectively, in the uptake of water and mineral nutrients and in nitrogen fixation. Since both organs have considerable impacts on plant growth, understanding the mechanisms underlying the development of lateral roots and nodules is crucial to improve agronomical traits in legumes. MicroRNA390 (miR390) is an evolutionarily conserved miRNA that targets non-coding Trans Acting Short Interference RNA3 (TAS3). Cleavage of TAS3 by ARGONAUTE7 results in the production of tasiRNAs, which target mRNAs encoding AUXIN RESPONSE FACTOR 2 (ARF2), ARF3 and ARF4. The miR390/TAS3 pathway plays key roles in plant development. tasiARFs suppress the juvenile to adult phase transition in Arabidopsis (Arbidopsis thaliana) and are required for leaf patterning and leaf polarity in different plant species, including the two model leguminous plants L. japonicus and M. truncatula. The miR390/TAS3 pathway also defines a network that quantitatively controls lateral root growth in Arabidopsis. Hobecker et al. (10.1104/pp.17.00464) now show that the activation of the miR390/TAS3 regulatory module by overexpression of miR390 in Medicago truncatula promotes lateral root growth, but prevents nodule organogenesis, rhizobial infection and the induction of two key nodulation genes. Accordingly, inactivation of the miR390/TAS3 module, either by expression of a miR390 target mimicry construct or mutations in ARGONAUTE7, enhances nodulation and rhizobial infection, alters the spatial distribution of the nodules and increases the percentage of nodules with multiple meristems. These results reveal a key role of the miR390/TAS3 pathway in legumes as a modulator of lateral root organs, playing opposite roles in lateral root and nodule development.

A Key Enzyme in the Biosynthesis of a Plant-Derived anti-HIV Drug

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Rhododendron dauricum (Ericaceae), a native of northeastern Asia, produces unique secondary metabolites including daurichromenic acid (DCA). DCA has attracted considerable attention as a medicinal resource because this compound is one of the most effective natural products with anti-HIV properties in cell culture.  Thus, chemical synthesis of DCA has been extensively studied over the past few years. Previously, a partial characterization has been made of an oxidocyclase, named DCA synthase, using a crude protein extract from young leaves of R. dauricum. DCA synthase is an enzyme that catalyzes the stereoselective oxidative cyclization of farnesyl moiety of grifolic acid to form DCA. Unlike P-450 type cyclases involved in glyceollin and furanocoumarin biosynthesis, DCA synthase is a soluble protein, and does not need exogenously added cofactors for the reaction. Remarkably, these features are similar to those reported for cannabinoid synthases from Cannabis sativa. Iijima et al. (10.1104/pp.17.00586) isolated the cDNA of the gene encoding DCA synthase, based on homology search against translated R. dauricum young leaf transcriptome, using cannabinoid synthases as queries. Heterologous expression of the recombinant proteins in a Pichia pastoris system provided the evidence that one of the candidate cDNAs is of a gene that encodes an active DCA synthase. Previously, the authors have shown that relevant metabolites as well as DCA synthase activity are predominantly localized to young leaves of R. dauricum that are covered with multicellular trichomes called glandular scales. The authors provide evidence that DCA, a phytotoxic metabolite, is primarily biosynthesized in the glandular scales of young leaves and accumulated extracellularly.

BEN, ROB, and the Making of a Petunia Flower

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A lot of effort goes into making a flower. Suites of genes must function in the right place at the right time. If not, stamens might grow where sepals should be, and so on, yielding homeotic mutant flowers. In general, flower parts are arranged in four concentric whorls of organs, including (from outside to inside) sepals, petals, stamens, and carpels. Three classes of genes specify floral organ formation: organ-identity genes that activate downstream organ-specific gene expression; boundary-setting genes that restrict the expression of specific genes to the appropriate whorl; and genes required for the initial activation of organ-identity genes. Extensive homeotic mutant analysis gave rise to the venerable ABC model (reviewed in Weigel and Meyerowitz, 1994). Each whorl of a flower is specified by a unique combination of organ identity activities: function A for sepals, A and B for petals, B and C for stamens, and C for carpels. Function A and C mutually repress each other and are carried out by both organ-identity and boundary-setting genes.

B- and C-function genes are conserved in a wide variety of plants, including the rosid species Arabidopsis thaliana and the astrid species Petunia hybrida. However, while the A-function transcription factor gene APETALA2 (AP2) has both organ identity and boundary-setting activities in Arabidopsis (e.g., Wollmann et al. 2010) and acts as the major repressor of C-activity in the outer floral whorls, the equivalent C-repressor function in petunia is encoded by the microRNA BLIND (BL), which likely represses the activity of NF-YA transcription factors (Cartolano et al., 2007). Intriguingly, while petals are converted into stamen-like structures in bl mutants due to the combined expression of B- and C-function genes in the second whorl, the expression of C-function genes in the first whorl does not lead to the conversion of sepals to carpels as predicted by the ABC model, implying that factors besides BL also repress the C-function to prevent carpel development in the first floral whorl of petunia.

Prompted by this finding, Morel et al. (2017) took advantage of a petunia line with abundant dTph1 transposons to uncover a mechanism controlling the spatial restriction of floral organ-identity genes in petunia. The authors introgressed the bl mutation into this dTph1 line to create new, transposon-tagged mutants. Screening this population for mutations that enhance the bl phenotype led to the identification of ben (for blind enhancer) mutants in the bl background. In ben bl mutants, all sepals are converted into carpels and C-class genes are expressed at high levels. By contrast, ben single mutants exhibit only subtle sepal defects, with varying degrees of petaloid sepals, pointing to a possible role for BEN in preventing B-class gene expression in sepals. Analysis of a single dTph1-tagged mutation that fully cosegregated with the ben phenotype revealed that BEN corresponds to the functionally uncharacterized TOE-type AP2B gene, whereas TOE-type genes in Arabidopsis control flowering time. Therefore, C-function repression in petunia sepals is controlled by two divergent parallel mechanisms compared to Arabidopsis: BL- and BEN-mediated repression. Mining of the petunia genome revealed three genes closely related to Arabidopsis AP2, the ROB (REPRESSOR OF B-FUNCTION) genes, which repress the B-function (but not the C-function) in the first floral whorl, together with BEN. Thus, ben bl rob mutants should have stamen-like structures where sepals should be, which is indeed the case (see figure).

While some of the underlying mechanisms appear to have diverged, floral formation in both rosid and astrid species is complicated, fascinating, and essential for plant reproduction.

 

REFERENCES

Cartolano, M., Castillo, R., Efremova, N., Kuckenberg, M., Zethof, J., Gerats, T., Schwarz-Sommer, Z., and Vandenbussche, M. (2007). A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity. Nature Genetics 39: 901–905.

Morel, P., Heijmans, K., Rozier, F., Zethof, J., Chamot, S., Bento, S. R., Vialette-Guiraud, A., Chambrier, P., Trehin, C., and Vandenbussche, M. (2017). Divergence of the floral A-function between an Asterid and a Rosid species. Plant Cell 29: doi:10.1015/tpc17.00098.

Weigel, D. and Meyerowitz, E.M. (1994). The ABCs of floral homeotic genes. Cell 78: 203–209.

Wollmann, H., Mica, E., Todesco, M., Long, J.A., and Weigel, D. (2010). On reconciling the interactions between APETALA2, miR172, and AGAMOUS with the ABC model of flower development. Development 137: 3633–3642.

The Who, What, and Where of Plant Polyprenol Biosynthesis Point to Thylakoid Membranes and Photosynthetic Performance

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Isoprenoids are a huge group of compounds that include primary metabolites such as carotenoids, chlorophylls, and hormones, as well as a plethora of specialized secondary metabolites. In addition to their importance in the physiology of plants (and of other kingdoms of life), isoprenoids have drawn attention in recent years for their applications in human health (reviewed in Kirby and Keasling, 2009). Isoprenoids are produced from two common 5-carbon isomers, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP; reviewed in Vranová et al., 2013) that serve as the building blocks for isoprenoids. The polyisoprenoids dolichol and polyprenol comprise a class of long, linear isoprenoids greater of 45 carbons or greater (see Figure). Whereas dolichols are well known for being essential in N-glycosylation, the functions of plastid-localized polyprenols are less clear (reviewed in Surmacz and Swiezewska, 2011). New work from Akhtar et al. (2017) exploring the biosynthesis of polyprenols in plants indicates that they could be important in thylakoid membrane dynamics.

A two-component complex required for dolichol synthesis (Brasher et al. 2015) in plants includes a cis-prenyltranferase (CPT), prompting Akhtar and coworkers to search among the nine Arabidopsis thaliana CPTs for those expressed in green tissue—where polyprenols are known to accumulate—and phylogenetically distinct from the CPT that produces dolichol. These criteria led the authors to CPT7 as a candidate for polyprenol biosynthesis.

Akhtar et al. found that wild-type leaves contained medium-chain polyprenols, composed of 9–11 isoprenoid units (45–55 carbons), mostly as free alcohols. By contrast, a homozygous cpt7 T-DNA mutant was missing these classes of polyprenols and CPT7 RNAi lines were decreased for them, whereas CPT7 overexpressors had markedly increased or at least wild-type levels. Further, recombinant CPT7 was active in adding IPP units to all three tested intermediate substrates, with a strong preference for farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP).

As FPP and GGDP are produced in different locations within the cell (see Figure), Akhtar and coauthors characterized the subcellular localization of CPT7. A combination of immunodetection and in vivo localization of fluorescent protein fusions revealed CPT7 in the stromal fraction, where most of the medium-chain CPT activity in the chloroplast resides. Thus, it appears that CPT7 functions as the primary enzyme for stromal polyprenol biosynthesis.

However, polyprenols are quite hydrophobic, and Akhtar et al. reasoned that they are unlikely to accumulate in the aqueous environment of chloroplast stroma, despite the stromal localization of CPT7. Indeed, polyprenols were present mainly in the thylakoid membrane fraction of wild type chloroplasts. Consistent with this localization, the CPT7 RNAi and CPT7 overexpression lines had lower and higher levels, respectively, of medium-chain polyprenols in the thylakoid fractions.

Akhtar et al. took advantage of these lines to address the possible roles of polyprenols in the thylakoid membrane. In artificial membranes, polyprenols are reported to increase membrane fluidity. In the protein-dense thylakoid membranes, however, fluorescence anisotropy analysis revealed that the lines with less polyprenol had greater membrane fluidity. These lines also had lower photosystem II operating efficiency, due to a lower rate of electron transport. These analyses thus suggest that medium-chain polyprenols—produced by CPT7—help determine the biophysical characteristics of thylakoid membranes by restricting fluidity, with important consequences to photosynthetic performance.

REFERENCES

 

Akhtar, T.A., Surowiecki, P., Siekierska, H., Kania, M., Van Gelder, K., Rea, K., Virta, L., Maritza Vatta, Gawarecka, K., Wojcik, J., Danikiewicz, W., Buszewicz, D., Swiezewska, E., Surmacz, L. (2017). Polyprenols are Synthesized by a Plastidial cis-Prenyltransferase and Influence Photosynthetic Performance. Plant Cell. doi: 10.1105/tpc.16.00796.

Brasher, M.I., Surmacz, L., Leong, B., Pitcher, J., Swiezewska, E., Pichersky, E., Akhtar, T.A. (2015) A two-component enzyme complex is required for dolichol biosynthesis in tomato. Plant J. 82: 903-914.

Kirby, J., and Keasling, J.D. (2009) Biosynthesis of plant isoprenoids:  perspectives for microbial engineering. Annu. Rev. Plant. Biol. 60: 335-355.

Surmacz, L., and Swiezewska, E. (2011) Polyisoprenoids – Secondary metabolites or physiologically important superlipids? Biochem. Biophys. Res. Commun. 407: 627-632.

Vranová, E., Coman, D., and Gruissem, W. (2013) Network analysis of the MVA and MEP pathways for isoprenoid synthesis. Annu. Rev. Plant Biol. 64: 665-700.

What We’re Reading: July 28th

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This week’s edition of What We’re Reading is guest edited by Dr. Bhavisha P. Sheth, who is currently working as a DST- Science, Technology and Innovation Policy Postdoctoral Fellow at the Entrepreneurship Development Institute of India (EDII), India. Her current research work focusses on Policy research studies of Science and Technology Entrepreneurship. She pursued a PhD in Plant Biotechnology and her thesis was awarded ‘the Best Life Sciences PhD Thesis’ in the state. During her PhD, she was a recipient of the UGC Junior and Senior Research Fellowships from Govt. of India. She has published 15 papers in national and international journals of high repute as well as presented her research in various conferences in India and abroad.

Differentially regulated orthologs in sorghum and the subgenomes of maize

Gene expression patterns are often used to assign function, but how tight is the correlation between expression and function? Zhang et al. addressed this question by investigating whether orthologous genes in two species (including the two subgenomes of maize) show similar patterns of expression. Specifically, they carried out a genome-wide transcriptional comparison of cold-response in sorghum and maize. They found that most orthologous genes were not similarly regulated in maize and sorghum, although early-expressed cold-response genes showed greater cross-species conservation than later genes. Further, genes with conserved transcriptional regulation patterns had a low ratio of non-synonymous to synonymous substitutions, suggesting stronger selection. The authors suggest that cross-species expression comparisons can reveal functionally important genes. Plant Cell. 10.1105/tpc.17.00354

A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone ($)

By measuring the length of Arabidopsis and rice roots treated with synthetic peptides, Pruitt et al. showed that RaxX, a peptide produced by the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo), mimicked the growth-stimulating activity of plant peptides containing sulfated tyrosine residues (PSYs). They propose that the pathogen produces RaxX to promote growth of infected tissues, and they also show that RaxX-deficient Xanthomonas have decreased virulence. Unlike growth-promoting PSYs, the pathogen-derived peptide induces immune responses, indicating that the plant is able to distinguish between the endogenous and pathogen-derived peptides. New Phytol. 10.1111/nph.14609

 

Rice peroxisomal ascorbate peroxidase knockdown affects ROS signaling and triggers early leaf senescence ($)

Ribeiro et al. describe functional aspects of the rice gene OsAPX4 encoding a peroxisomal ascorbate peroxidase, which shows the highest level of expression in leaves. RNAi silencing of this gene did not lead to an increase in the intracellular H2O2 levels and no change was observed in growing plants. However, a drastic change was seen in  aging plants which exhibited early senescence. The study suggests that OsAPX4 plays a significant role in ROS signalling during leaf senescence Plant Science. 10.1016/j.plantsci.2017.07.009

 

Heterologous expression of two GPATs from Jatropha curcas alters seed oil levels in transgenic Arabidopsis thaliana ($)

Mishra et al. (2017) characterized two GPATs (glycerol-3-phosphate acyltransferase) JcGPAT1 and JcGPAT2 in the biofuel seed oil crop Jatropha curcas. These GPATs showed sequence homology with Arabidopsis acyltransferase-1 (ATS1) and Arabidopsis GPAT (AtGPAT9) respectively. Subcellular localization studies indicated that JcGPAT1 is localized in plastids whereas JcGPAT2 is localized in the endoplasmic reticulum. Overexpression of these enzymes in Arabidopsis thaliana led to an increase in total seed oil content – as much as a 43-60% increase in transgenic lines overexpressing JcGPAT2. This study highlights the role of these GPATs in oil biosynthesis in Jatropha curcas. Plant Science 10.1016/j.plantsci.2017.07.003  Image source: Elitre

 

Phylogenetic analysis of proteins involved in the stringent response in plant cells ($)

The stringent response in bacteria is a global transcriptional response to stress, mediated by the second messenger ppGpp (guanosine 5′-diphosphate 3′-diphosphate) which is synthesized by the action of guanosine 5′-triphosphate 3′-diphosphate pyrophosphatase (GppA) or exopolyphosphatase (Ppx). Recently it was shown that plants also exhibit a stringent response mediated by ppGpp, but the origin of this response in plants has not been resolved.  Ito et al. investigated the distribution of the gppA/ppx gene families as well as the RSH hydrolase gene family. Their data indicate that genes involved in the stringent response were likely introduced to plants from various bacterial phyla by lateral gene transfer events. Moreover, the results suggest that plant RSH homologs likely function in the plastid, whereas the plant gppA/ppx homologs may function in the cytosol. J. Plant Research 10.1007/s10265-017-0922-8

 

Structure and expression patterns of dehydrin gene family in barley ($)

Dehydrins are proteins that have important roles in dehydration stress in plants. Abedini et al. carried out a phylogenetic analysis of barley dehydrins and investigated physiological and gene expression levels in tolerant (HV1), and susceptible (HV2) cultivars and a drought tolerant Iranian wild barley genotype (Spontaneum; HS) subjected to water stress and after recovery. They found notable differences in physiological responses and dehydrin expression levels in the drought tolerant varieties as compared to the susceptible variety, as well as between the wild and cultivated genotypes, supporting the role for dehydrins in vegetative drought tolerance. As barley is an important grain in arid regions, the study will contribute to future breeding efforts for drought tolerance J. Plant Research 10.1007/s10265-017-0941-5.

 

Identification and functional analysis of new peroxygenases in oat ($)

Peroxygenases catalyze the hydroperoxide dependent epoxidation of unsaturated fatty acids. Benaragama et al. identified two novel peroxygenases (AsPXG2 and AsPXG3) in oat (Avena sativa L.) AsPXG2 and AsPXG3 share structural similarity by having a single transmembrane domain, conserved histidines for heme-binding as well as a conserved EF-hand motif. However, they show only 50% amino acid identity with each other, and the activity of heterologously-expressed AsPXG3 is much higher than that of AsPXG2. Site-directed mutagenesis of AsPXG3 showed that replacement of two conserved histidines by alanine resulted in complete loss of activity, and substitution of three conserved residues surrounding the two histidines resulted in reduction of enzymatic activity by more than 80%, suggesting that these conserved residues are located near the catalytic sites, where they coordinate the heme group and define the shape and size of the catalytic site. Planta 10.1007/s00425-017-2729-1.

 

Vesicle dynamics during plant cell cytokinesis reveals distinct developmental phases

The cell plate is a common feature of plant cell divisions, but the mechanisms forming this structure are not completely understood.  The cell plate is made from membrane vesicles carrying polysaccharide cargo, and thousands of tiny vesicles fuse together to form one cell plate.  Observing fluorescence micrographs alone cannot provide a full picture of cell plate biogenesis, so Oostende-Triplet et al. developed FluMOS (Fluorescence Morphological Operators Software).  This program can identify and analyze cell plates within fluorescence confocal images.  The authors identified three distinct phases of cell plate expansion in N. tabacum BY-2 cells based on the growth rate of the cell plate.  FluMOS quantitated vesicle movement towards nascent cell plates.  Initially, the vesicles move quickly to the cell plate when its growth begins.  As the cell plate growth, vesicle movement remains high at the edges, but vesicle movement slows in the center of the cell plate.  Pharmacological inhibition of membrane trafficking and protein synthesis showed both processes contribute to cell plate expansion. (Summary by Daniel Czerny) Plant Physiol. 10.1104/pp.17.00343

Are you interested in contributing to What We’re Reading? We welcome informal, one-off summaries, but you can also formalize your contributions by applying to be a Plantae Fellow, like Daniel and Bhavisha are!

 

A Taste of CRISPR

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This week’s blog was written by Dr Craig Cormick, the Creative Director of ThinkOutsideThe. He is one of Australia’s leading science communicators, with over 30 years’ experience working with agencies such as CSIRO, Questacon and Federal Government Departments.

 

So what do you think CRISPR cabbage might taste like? CRISPR-crispy? Altered in some way?

Participants at the recent Society for Experimental Biology/Global Plant Council New Breeding Technologies workshop in Gothenburg, Sweden, had a chance to find out, because in Sweden CRISPR-produced plants are not captured by the country’s regulations for GMOs and can be produced.

Professor Stefan Jansson, one of the workshop organizers, has grown the CRISPR cabbage (discussed in his blog for GPC!) and not only had it included on the menu of the workshop dinner, but had samples for participants to take away. Some delegates were keen to pick up the samples while others were unsure how their own country’s regulatory rules would apply to them.

 

Click here to read the rest of this post on the Global Plant Council blog.