Interaction between Bms1 and Rcl1,two ribosome biogenesis factors,is evolutionally conserved in zebrafish and human

正Ribosomes are large RNA and protein complexes that function as the machinery for translation protein synthesis(Boisvert et al.,2007;Ben-Shem et al.,2011;Henras et al.,2015;Khatter et al.,2015;McCann et al.,2015).The eukaryotic ribosome is composed of two subunits,the 60S large subunit(LSU)and the 40S small subunit(SSU),which collectively comprise of four different ribosomal RNA(rRNA)species and more than 70 proteins(Ben-Shem et al.,2011;Henras et al.,2015;Khatter et al.,2015).The LSU contains     

Resolving the Activation Site of PositiveRegulators in Plant PhosphoenolpyruvateCarboxylase

Dear Editor, Phosphoenolpyruvate carboxylase （PEPC; EC 4.1.1.31） islocated at an important branch point in the carbohydratemetabolism of plants. The enzyme is a homotetramer andcatalyzes the addition of bicarbonate to phosphoenolpyru-vate （PEP） to form oxaloacetate and phosphate. PEPC isregulated by metabolites and phosphorylation. AIIostericfeedback inhibition is mainly regulated by L-malate andL-aspartate which bind to a site separated from the activecenter （Kai et al., 1999; Paulus et al., 2013）. Structure analy-sis of PEPC from Escherichia coli （Kai et al., 1999; Matsumuraet al., 2002）, Zea rnays （Matsumura et al., 2002）, Flaveria trin-ervia, and F. pringlei （Paulus et al., 2013） revealed that thesubstrate PEP and the feedback inhibitors bind to separatesites within each monomer.     

Intracellular NHX-Type Cation/H＋ Antiporters inPlants

Cells depend on the homeostatic maintenance of pHwithin specific cellular compartments to ensure optimalconditions for metabolic and enzymatic processes as wellas protein structure and function. In the animal secre-tory pathway, cells maintain distinct luminal pHs withinvarious compartments （Paroutis et al., 2004）. Among themany molecular players that contribute to pH and ionhomeostasis in plants, Na＋（K＋）/H＋ exchangers （also knownas NHX-type cation/H＋ antiporters） appear to be particu-larly important for the regulation of a wide variety ofphysiological processes, including cell expansion, cellvolume regulation, osmotic adjustment, pH regulation,membrane trafficking, protein processing, and cellularstress responses （Pardo et al., 2006; Rodriguez-Rosaleset al., 2009; Bassil et al., 2012）. In plants, NHX antiportersappeared early in evolution and are ubiquitously encodedmembers of the CPA1 cation/H＋ antiporters subgroupthat belongs to the large family of monovalent cation/H＋ transporters CPA （Brett et al., 2005）. NHX antiport-ers are found, thus far, in all sequenced plant genomes（Bassil et al., 2012; Chanroj et al., 2012）. In Arabidopsis,the NHX family consists of eight isoforms, six of whichare intracellular （AtNHXl-AtNHX6）, located either to thevacuole （AtNHXl to AtNHX4） or endosomes （AtNHX5 andAtNHX6） and an additional two more divergent members（AtNHX7/SOSl and AtNHX8） at the plasma membrane（Bassil et al., 2012）. Orthologous sequences in each of thethree classes （plasma membrane, vacuolar, or endosomal）appear in all sequenced genomes, suggesting that distinctfunctional NHX classes appeared early in evolution andmay have conserved roles that are compartment-specific（Bassil et al., 2012）. Emerging new evidence highlightsthe importance of particular intracellular NHX antiport-ers in the regulation of vesicular and vacuolar pH andK＋ homeostasis. Vacuolar NHXs are needed to maintainK＋ homeostasis between the vacuole and cytosol, with-out which cell expansion is compromised （Bassil et al.,2011b）. Other NHX isoforms （endosomal） are requiredfor membrane trafficking and raise interesting new ques-tions about the role of pH and ion homeostasis in proteinprocessing and trafficking in the endomembrane system（Bassil et al., 2011a）. In this update, we aim to highlightrecent new evidence on intracellular NHX antiportersand emphasize possible novel and important cellular pro-cesses regulated by this particularly interesting group oftransporters.     

Terminal transfer amplification and sequencing for high-efficiency and lowbias copy number profiling of fragmented DNA samples

Dear Editor,Since its invention,next generation sequencing(NGS)has greatly facilitated biomedical research and clinical diagnosis(Sikkema-Raddatz et al.,2013).Continuous dropping of the cost further accelerated the adaptation of sequencing as a standard analytical tool,from identification of drug candidates(Walker et al.,2015)to deciphering the complex biological systems(McConnell et al.,2013).     

The Conserved Proline Residue in the LOB Domain of LBD18 Is Critical for DNA-Binding and Biological Function

Dear Editor, The LATERAL ORGAN BOUNDARIES DOMAIN （LBD）/ ASYMMETRICLEAVES2-LIKE （ASL） genes （hereafter referred to as LBD） encode proteins containing a conserved plant-specific LOB domain and play roles in lateral organ development （Iwakawa et al., 2002; Shuai et al., 2002; Majer and Hochholdinger, 2011）. The LOB domain is approximately 100 amino acids in length and contains a conserved four-Cys motif （CX2CX6CX3C）, the Gly-Ala-Ser block （GAS）, and the leucine-zipper-like coiled-coil motif （LX6LX3LX6L） （Shuai et al., 2002）. The leucine-zipper-like coiled-coil motif in the LOB domain is predicted to function in protein dimerization. LOB, AS2, and LBD4 preferentially bind unique DNA sequences in electrophoretic mobility shift assays （EMSAs） （Husbands et al., 2007）. The LOB domain of AS2 cannot be functionally replaced by those of other members of the LOB family,     

PhGRL2 Protein,Interacting with PhACO1, Is Involved in Flower Senescence in the Petunia

Dear Editor, The pathways of ethylene biosynthesis and signaling have been studied in detail （Ji and Guo, 2013）. Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 （RTE1）, interacting with ETR1, and its homologs tomato GREEN RIPE （SlGR） and SlGRL1, and rice OsRTH1 negatively regulate the ethylene signaling （Barry and Giovannoni, 2006, Resnick et al., 2006; Dong et al., 2010; Zhang et al., 2012）. A newly published study suggested that a cytochrome b5 and RTE1 are functional partners in promoting ETRl-mediated repression of ethylene signaling in Arabidopsis （Chang et al., 2014）. However, AtRTH, RTE1 homolog in Arabidopsis, and its closest homolog in the tomato, SlGRL2 （GR-like2）, do not play a role in ethylene signaling （Dong et al., 2010）, and the function of the homologs of these members is not well known.     

A Start Point for Extracellular Nucleotide Signaling

A START POINT FOR EXTRACELLULAR NUCLEOTIDE SIGNALING
The recent discovery of a plant receptor for extracellu- lar nucleotides, reported by Choi et al. （2014）, is a major breakthrough that had been anticipated for over a dec- ade. Plants release ATP into their extracellular matrix （ECM） during growth and when they are induced by vari- ous biotic and abiotic stimuli （Clark and Roux, 2011）. That these extracellular nucleotides would activate receptors in plants was predicted by two sets of discoveries： that low- and sub-micromolar ATP could induce increases in [Ca2＋]cyt, NO, and superoxide signaling intermediates that led to downstream growth, stomatal, and defense responses, and that these changes could be blocked by antagonists that blocked extracellular nucleotide receptors in animals （Demidchik et al., 2003; Song et al., 2006; Clark et al., 2011; Demidchik et al., 2009, 2011）. Although mammalian biolo- gists had discovered two classes of receptors for extracel- lular nucleotides （P2X and P2Y） decades ago （Burnstock, 2007）, there were no plant proteins obviously similar to these in any sequence data available. Clearly, if there were plant purinoceptors, they would be different from the mammalian receptors, and they could not be discovered by motif searches.     

The post-genomics era of cotton

正As one of the important industrial crops and also an excellent model organism for studying cell elongation,cell wall biosynthesis as well as polyploidy evolution,cotton has always been in the limelight of the world(Shi et al.,2006;Qin and Zhu,2011).With the publication of the allotetraploid Gossypium hirsutum and Gossypium barbadense genomes this year(Li et al.,2015;Zhang et al.,2015;Liu et al.,2015),all three important cotton genomes,including the two ancestor diploid Gossypium raimondii(DD)(Wang et al.,2012;Paterson et al.,2012)and Gossypium arboreum(AA)(Li et al.,2014)have been successfully sequenced by scientists from China and from the United States of America.Since functional studies of Arabidopsis thaliana and     

A Brassinosteroid-Signaling Kinase Interacts withMultiple Receptor-Like Kinases in Arabidopsis

Dear Editor, Higher plants have evolved hundreds of genes encodingreceptor-like kinases （RLKs）, which function as cell surfacereceptors perceiving developmental and environmental sig-nals （Shiu et al., 2004）. Many RLKs have been shown to playspecific roles in hormone responses, developmental regula-tion, defense against pathogen infection, and adaptationto abiotic stresses （Chae et al., 2009; Antolin-Llovera et al.,2012）. The mechanisms that ensure specific signal transduc-tion from each RLK to target cellular responses remain poorlyunderstood. Recent studies revealed that many RLKs trans-duce signals by phosphorylating receptor-like cytoplasmickinases （RLCKs）, which lack the transmembrane domainsbut are anchored at the plasma membrane through lipidmodification （Tang et al., 2008; Zhang et al., 2010; Shi et al.,2013）. There are over 400 RLKs and only about 150 RLCKs inArabidopsis （Shiu et al., 2004）. One outstanding question iswhether each RLCK mediates signaling downstream of a spe-cific RLK, participates in multiple RLK pathways, or mediatescrosstalk between RLK pathways.     

Efficient Gene Targeting in Zebrafish Mediated by a Zebrafish-Codon-Optimized Cas9 and Evaluation of Off-Targeting Effect

Targeted genome modifications with the Cas9/gRNA system derived from the clustered regularly interspaced short palin- dromic repeat/CRISPR-associated （CRISPR/Cas） system have been successfully used in cultured human cells as well as in most model organisms, including zebrafish （Danio rerio）, mouse, and fruit fly （Chang et al., 2013; Cong et al., 2013; Gratz et al., 2013; Hwang et al., 2013; Jao et al., 2013; Shen et al., 2013; Wei et al., 2013）. Its application in zebrafish is particu- larly attractive due to the ease of handling this organism and the simple application of this method by direct injection of Cas9/ gRNA. However, the information about its specificity in this organism is very limited and needs further evaluation. In addition, it is conceivable that a Cas9 mRNA optimized for zebrafish codon preference could enhance its activity.     

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

Heterosis,one of the most important biological phenomena,refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass,growth rate and yield.Despite its successful application in breeding and agronomic production of many crop and animal varieties,the molecular basis of heterosis remains elusive.The classic genetic explanations for heterosis centered on three hypotheses:dominance (Davenport,1908;Bruce,1910;Keeble and Pellew,1910;Jones,1917),overdominance (East,1908;Shull,1908) and epistasis (Powers,1944;Yu et al.,1997).However,these hypotheses are largely conceptual and not connected to molecular principles,and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al.,2003).Recently,many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level.These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g.,Swanson-Wagner et al.,2006;Zhang et al.,2008;Wei et al.,2009;Song et al.,2010).Research suggests that genetic components,including cis-acting elements and trans-acting factors,are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker,2007;Springer and Stupar,2007;Zhang et al.,2008).However,other research indicates that epigenetic components,the regulators of chromatin states and genome activity,also have the potential to impact heterosis (e.g.,Ha et al.,2009;He et al.,2010;Groszmann et al.,2011;Barber et al.,2012;Chodavarapu et al.,2012;Greaves et al.,2012a;Shen et al.,2012).     

Drosophila protein phosphatase V regulates lipic homeostasis via the AMPK pathway

Dear Editor, Protein phosphorylation is essential for multiple cellular processes. This post- translational modification is regulated by kinase-mediated phosphorylation and phosphatase-mediated dephosphorylation. Drosophila protein phosphatase V （PpV） and Saccheromyces cerevisiae Sit4 are homologs of mammalian PP6, which belongs to the PP2A subfamily of serine/threonine phosphatases （Mann et al., 1993; Wang et al., 2012）. In addition to the catalytic subunit, PP6 holoenzyme also contains a regulatory subunit （PP6R1-, PP6R2, or PP6R3 in human; Sap4, Sap1-55, Sap1_85, or Sap190 in yeast; CG10289 in fly） and a scaffold subunit （Morales-lohansson et al., 2009）. Studies in 5. cerevisiee showed that 5it4 knockout strain had reduced lipid droplet content and increased phosphoryl- ation of SNF1- （a homolog of mammalian and Drosophila AMPK） at an evolutionally conserved activation site （BozaqueI-Morais et al., 2010; Ruiz et a[., 2011）. However, its function in metazoan has not been well explored.     

Using the inverse Poisson distribution to calculate multiplicity of infection and viral replication by a high-throughput fluorescent imaging system

正Dear Editor,For virologists,it is crucial to confidently determine the concentration of infectious particles that are utilized and produced in experiments(Dulbecco,1952;Bushar and Sagripanti,1990;La Barre and Lowy,2001;Gueret et al.,2002;Gao et al.,2009;Kutner et al.,2009;Grigorov et al.,2011;Knipe and Howley,2013).With respect to     

Positive Selection of CAG Repeats of the ATXN2 Gene in Chinese Ethnic Groups

The ataxin-2 （ATXN2） gene is located on human chromo-some 12q24.1. In normal individuals, the coding region in exon 1 of this gene has fewer than 31 CAG repeats （Yu et al., 2005： Laffita-Mesa et al., 2012）. However, an abnormal expansion of CAG trinucleotide repeats results in the aggre-gation of polyglutamine （polyQ）, which causes spinocer-ebellar ataxia type 2 （SCA2） （Pulst et al., 1996）. The expanded alleles have more than 32 repeats in the affected individuals, and generally there is an inverse correlation between CAG repeat length and age of onset （Pulst et al., 1996）. SCA2 is an autosomal dominant inheritance neurodegenerative disease, whose major clinical feature is progressive cerebellar ataxia. Atrophies of the brainstem and frontal lobe have been frequently detected by magnetic resonance imaging （MRI） （Yamamoto-Watanabe et al., 2010）. This disease has the strong effect on sensory and motor control.     

To Grow or Not to Grow： FERONIA Has Her Say

Plant cells differ from their animal counterparts such that they are encased in a complex wall structure, crucial for cell growth through a dynamic equilibrium of rigidity and flexibility. Cell wall extensibility can be greatly influenced by apoplastic pH and reactive oxygen species （ROS） （Duan et al., 2014; Haruta et al., 2014）. Several recent works demonstrated that the receptor-like kinase （RLK） FERONIA （FER） is critical to fine-tune cell growth in a spatiotemporal and context-dependent manner by controlling apoplastic pH （Haruta et al., 2014） and ROS （Duan et al., 2010, 2014）, likely balancing wall rigidity for cell integrity and flexibility for cell expansion.     

Synthetic genomes engineered by SCRaMbLEing

正The ability to design and synthesize the genome of a living organism marks one of the most significant achievements in synthetic biology.The first synthetic genomes were those of bacteria(Gibson et al.,2010;Hutchison et al.,2016),but an international consortium of scientists is now undertaking the ambitious task of designing and synthesizing the entire genome of Saccharomayces cerevisiae,a eukaryotic singlecelled yeast(Dymond et al.,2011;Kannan and Gibson,2017).One feature of the redesigned yeast genome,called