Intercellular and intracellular signalling systems that globally control the expression of virulence genes in plant pathogenic bacteria

Plant pathogenic bacteria utilize complex signalling systems to control the expression of virulence genes at the cellular level and within populations. Quorum sensing (QS), an important intercellular communication mechanism, is mediated by different types of small molecules, including N‐acyl homoserine lactones (AHLs), fatty acids and small proteins. AHL‐mediated signalling systems dependent on the LuxI and LuxR family proteins play critical roles in the virulence of a wide range of Gram‐negative plant pathogenic bacteria belonging to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Xanthomonas spp. and Xylella fastidiosa, members of the Gammaproteobacteria, however, possess QS systems that are mediated by fatty acid‐type diffusible signal factors (DSFs). Recent studies have demonstrated that Ax21, a 194‐amino‐acid protein in Xanthomonas oryzae pv. oryzae, plays dual functions in activating a rice innate immune pathway through binding to the rice XA21 pattern recognition receptor and in regulating bacterial virulence and biofilm formation as a QS signal molecule. In xanthomonads, DSF‐mediated QS systems are connected with the signalling pathways mediated by cyclic diguanosine monophosphate (c‐di‐GMP), which functions as a second messenger for the control of virulence gene expression in these bacterial pathogens.     

The development and status of Bt rice in China

Multiple lines of transgenic rice expressing insecticidal genes from the bacterium Bacillus thuringiensis (Bt) have been developed in China, posing the prospect of increases in production with decreased application of pesticides. We explore the issues facing adoption of Bt rice for commercial production in China. A body of safety assessment work on Bt rice has shown that Bt rice poses a negligible risk to the environment and that Bt rice products are as safe as non‐Bt control rice products as food. China has a relatively well‐developed regulatory system for risk assessment and management of genetically modified (GM) plants; however, decision‐making regarding approval of commercial production has become politicized, and two Bt rice lines that otherwise were ready have not been allowed to enter the Chinese agricultural system. We predict that Chinese farmers would value the prospect of increased yield with decreased use of pesticide and would readily adopt production of Bt rice. That Bt rice lines may not be commercialized in the near future we attribute to social pressures, largely due to the low level of understanding and acceptance of GM crops by Chinese consumers. Hence, enhancing communication of GM crop science‐related issues to the public is an important, unmet need. While the dynamics of each issue are particular to China, they typify those in many countries where adoption of GM crops has been not been rapid; hence, the assessment of these dynamics might inform resolution of these issues in other countries.     

Rice copine genes OsBON1 and OsBON3 function as suppressors of broad‐spectrum disease resistance

Breeding for disease resistance is the most effective strategy to control diseases, particularly with broad‐spectrum disease resistance in many crops. However, knowledge on genes and mechanism of broad‐spectrum resistance and trade‐off between defence and growth in crops is limited. Here, we show that the rice copine genes OsBON1 and OsBON3 are critical suppressors of immunity. Both OsBON1 and OsBON3 changed their protein subcellular localization upon pathogen challenge. Knockdown of OsBON1 and dominant negative mutant of OsBON3 each enhanced resistance to rice bacterial and fungal pathogens with either hemibiotrophic or necrotrophic lifestyles. The defence activation in OsBON1 knockdown mutants was associated with reduced growth, both of which were largely suppressed under high temperature. In contrast, overexpression of OsBON1 or OsBON3 decreased disease resistance and promoted plant growth. However, neither OsBON1 nor OsBON3 could rescue the dwarf phenotype of the Arabidopsis BON1 knockout mutant, suggesting a divergence of the rice and Arabidopsis copine genes. Our study therefore shows that the rice copine genes play a negative role in regulating disease resistance and their expression level and protein location likely have a large impact on the balance between immunity and agronomic traits.     

A yeast‐based rapid prototype platform for gene control elements in mammalian cells

Programming genetic circuits in mammalian cells requires flexible, tunable, and user‐tailored gene‐control systems. However, most existing control systems are either mechanistically specific for microbial organisms or must be laboriously re‐engineered to function in mammalian cells. Here, we demonstrate a ribozyme‐based device platform that can be directly transported from yeast to mammalian cells in a “plug‐and‐play” manner. Ribozyme switches previously prototyped in yeast are shown to regulate gene expression in a predictable, ligand‐responsive manner in human HEK 293, HeLa, and U2OS cell lines without any change to device sequence nor further optimization. The ribozyme‐based devices, which exhibit activation ratios comparable to the best RNA‐based regulatory devices demonstrated in mammalian cells to‐date, retain their prescribed functions (ON or OFF switch), tunability of regulatory stringency, and responsiveness to different small‐molecule inputs in mammalian hosts. Furthermore, we observe strong correlations of device performance between yeast and all mammalian cell lines tested (R² = 0.63–0.97). Our unique device architecture can therefore act as a rapid prototyping platform (RPP) based on a yeast chassis, providing a well‐developed and genetically tractable system that supports rapid and high‐throughput screens for generating gene‐controllers with a broad range of functions in mammalian cells. This platform will accelerate development of mammalian gene‐controllers for diverse applications, including cell‐based therapeutics and cell‐fate reprogramming. Biotechnol. Bioeng. 2013; 110: 1201–1210. © 2012 Wiley Periodicals, Inc.     

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de‐domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de‐domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black‐coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw‐coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4‐coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de‐domestication.     

A mitogen‐activated protein kinase phosphatase influences grain size and weight in rice

Grain size and weight are directly associated with grain yield in crops. However, the molecular mechanisms that set final grain size and weight remain largely unknown. Here, we characterize two large grain mutants, large grain8‐1 (large8‐1) and large grain8‐2 (large8‐2). LARGE8 encodes the mitogen‐activated protein kinase phosphatase1 (OsMKP1). Loss of function mutations in OsMKP1 results in large grains, while overexpression of OsMKP1 leads to small grains. OsMKP1 determines grain size by restricting cell proliferation in grain hulls. OsMKP1 directly interacts with and deactivates the mitogen‐activated protein kinase 6 (OsMAPK6). Taken together, we identify OsMKP1 as a crucial factor that influences grain size by deactivating OsMAPK6, indicating that the reversible phosphorylation of OsMAPK6 plays important roles in determining grain size in rice.     

Rice siR109944 suppresses plant immunity to sheath blight and impacts multiple agronomic traits by affecting auxin homeostasis

Plant small RNAs (sRNAs) play significant roles in regulating various developmental processes and hormone signalling pathways involved in plant responses to a wide range of biotic and abiotic stresses. However, the functions of sRNAs in response to rice sheath blight remain unclear. We screened rice (Oryza sativa) sRNA expression patterns against Rhizoctonia solani and found that Tourist‐miniature inverted‐repeat transposable element (MITE)‐derived small interfering RNA (siRNA) (here referred to as siR109944) expression was clearly suppressed upon R. solani infection. One potential target of siR109944 is the F‐Box domain and LRR‐containing protein 55 (FBL55), which encode the transport inhibitor response 1 (TIR1)‐like protein. We found that rice had significantly enhanced susceptibility when siR109944 was overexpressed, while FBL55 OE plants showed resistance to R. solani challenge. Additionally, multiple agronomic traits of rice, including root length and flag leaf inclination, were affected by siR109944 expression. Auxin metabolism‐related and signalling pathway‐related genes were differentially expressed in the siR109944 OE and FBL55 OE plants. Importantly, pre‐treatment with auxin enhanced sheath blight resistance by affecting endogenous auxin homeostasis in rice. Furthermore, transgenic Arabidopsis overexpressing siR109944 exhibited early flowering, increased tiller numbers, and increased susceptibility to R. solani. Our results demonstrate that siR109944 has a conserved function in interfering with plant immunity, growth, and development by affecting auxin homeostasis in planta. Thus, siR109944 provides a genetic target for plant breeding in the future. Furthermore, exogenous application of indole‐3‐acetic acid (IAA) or auxin analogues might effectively protect field crops against diseases.     

Helicobacter pylori HtrA is a new secreted virulence factor that cleaves E‐cadherin to disrupt intercellular adhesion

Mammalian and prokaryotic high‐temperature requirement A (HtrA) proteins are chaperones and serine proteases with important roles in protein quality control. Here, we describe an entirely new function of HtrA and identify it as a new secreted virulence factor from Helicobacter pylori, which cleaves the ectodomain of the cell‐adhesion protein E‐cadherin. E‐cadherin shedding disrupts epithelial barrier functions allowing H. pylori designed to access the intercellular space. We then designed a small‐molecule inhibitor that efficiently blocks HtrA activity, E‐cadherin cleavage and intercellular entry of H. pylori.     

Simplified adenine base editors improve adenine base editing efficiency in rice

Adenine base editors (ABEs) have been exploited to introduce targeted adenine (A) to guanine (G) base conversions in various plant genomes, including rice, wheat and Arabidopsis. However, the ABEs reported thus far are all quite inefficient at many target sites in rice, which hampers their applications in plant genome engineering and crop breeding. Here, we show that unlike in the mammalian system, a simplified base editor ABE‐P1S (Adenine Base Editor‐Plant version 1 Simplified) containing the ecTadA*7.10‐nSpCas9 (D10A) fusion has much higher editing efficiency in rice compared to the widely used ABE‐P1 consisting of the ecTadA‐ecTadA*7.10‐nSpCas9 (D10A) fusion. We found that the protein expression level of ABE‐P1S is higher than that of ABE‐P1 in rice calli and protoplasts, which may explain the higher editing efficiency of ABE‐P1S in different rice varieties. Moreover, we demonstrate that the ecTadA*7.10‐nCas9 fusion can be used to improve the editing efficiency of other ABEs containing SaCas9 or the engineered SaKKH‐Cas9 variant. These more efficient ABEs will help advance trait improvements in rice and other crops.     

Control of flowering in rice through synthetic microProteins

Photoperiod‐dependent flowering in rice is regulated by HEADING DATE 1 (Hd1), which acts as both an activator and repressor of flowering in a daylength‐dependent manner. To investigate the use of microProteins as a tool to modify rice sensitivity to the photoperiod, we designed a synthetic Hd1 microProtein (Hd1miP) capable of interacting with Hd1 protein, and overexpressed it in rice. Transgenic OX‐Hd1miP plants flowered significantly earlier than wild type plants when grown in non‐inductive long day conditions. Our results show the potential of microProteins to serve as powerful tools for modulating crop traits and unraveling protein function.     

Discovery of rice essential genes by characterizing a CRISPR‐edited mutation of closely related rice MAP kinase genes

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein 9 nuclease (Cas9) system depends on a guide RNA (gRNA) to specify its target. By efficiently co‐expressing multiple gRNAs that target different genomic sites, the polycistronic tRNA‐gRNA gene (PTG) strategy enables multiplex gene editing in the family of closely related mitogen‐activated protein kinase (MPK) genes in Oryza sativa (rice). In this study, we identified MPK1 and MPK6 (Arabidopsis AtMPK6 and AtMPK4 orthologs, respectively) as essential genes for rice development by finding the preservation of MPK functional alleles and normal phenotypes in CRISPR‐edited mutants. The true knock‐out mutants of MPK1 were severely dwarfed and sterile, and homozygous mpk1 seeds from heterozygous parents were defective in embryo development. By contrast, heterozygous mpk6 mutant plants completely failed to produce homozygous mpk6 seeds. In addition, the functional importance of specific MPK features could be evaluated by characterizing CRISPR‐induced allelic variation in the conserved kinase domain of MPK6. By simultaneously targeting between two and eight genomic sites in the closely related MPK genes, we demonstrated 45–86% frequency of biallelic mutations and the successful creation of single, double and quadruple gene mutants. Indels and fragment deletion were both stably inherited to the next generations, and transgene‐free mutants of rice MPK genes were readily obtained via genetic segregation, thereby eliminating any positional effects of transgene insertions. Taken together, our study reveals the essentiality of MPK1 and MPK6 in rice development, and enables the functional discovery of previously inaccessible genes or domains with phenotypes masked by lethality or redundancy.     

A leader sequence capable of enhancing RNA expression and protein synthesis in mammalian cells

Many applications in biotechnology require human proteins generated from human cells. Stable cell lines commonly used for this purpose are difficult to develop, and scaling to large numbers of proteins can be problematic. Transient expression can circumvent this problem, but protein yields are generally too low for most applications. Here we report a novel 37‐nucleotide leader sequence that promotes rapid and high transgene expression in mammalian cells. This sequence was identified by in vitro selection and functions in a transient vaccinia‐based cytoplasmic expression system. Vectors containing this sequence produce microgram levels of protein in just 6 h from a small‐scale expression in 10⁶ cells. This level of protein synthesis is ideal for high throughput production of human proteins, and could be scaled to generate milligram quantities of protein. The technology is compatible with a broad range of cell lines, accepts plasmid and linear DNA, and functions with viruses that are approved for use under BSL1 conditions. We suggest that these advantages provide a powerful method for generating human protein in mammalian cells.     

Impacts of nitrogen fertilizer on major insect pests and their predators in transgenic Bt rice lines T2A‐1 and T1C‐19

Nitrogen is a critical factor for plant development and nitrogen input is one of the important tactics to enhance the development and yield of crops. Nevertheless, nitrogen input could influence the occurrence of insects positively or negatively. Nitrogen is also one of the main elements composing the insecticidal crystal (Cry) protein. Cry protein production could affect nitrogen partitioning in Bt plants and as such nitrogen input may influence insect pest management in transgenic Bt rice, Oryza sativa L. (Poaceae). To test this possibility, we evaluated the impacts of nitrogen regimes on the main insect pests and their predators on two Bt rice lines, T2A‐1 and T1C‐19, expressing Cry2A and Cry1C, respectively, and their non‐transgenic parental counterpart MH63. The results showed that Cry proteins with different nitrogen regimes have enough insecticidal activity on rice leaffolder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Crambidae), in both laboratory and field experiments. Laboratory studies indicated that relevant parameters of ecological fitness in brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), a non‐target insect pest, were significantly affected by nitrogen input both on Bt and MH63 rice lines. Nymphal survival, female adult longevity, and egg hatchability in N. lugens differed significantly among rice varieties. The experiments conducted in rice fields also demonstrated that nitrogen was positively correlated with the abundance of N. lugens on Bt rice, similar to that on MH63 rice. The abundances of two predators – the wolf spider Pirata subpiraticus (Boesenberg & Strand) (Araneae: Lycosidae) and the bug Cyrthorhinus lividipennis Reuter (Hemiptera: Miridae) – were significantly affected by rice growth stages but not by nitrogen input and rice varieties. In conclusion, the above results indicate that high nitrogen regimes for Bt rice (T2A‐1 and T1C‐19) and non‐Bt rice (MH63) cannot facilitate the management of insect pests.     

Transmission by Laodelphax striatellus Fallen of Rice black‐streaked dwarf virus from Frozen Infected Rice Leaves to Healthy Plants of Rice and Maize

Rice black‐streaked dwarf virus (RBSDV) is transmitted naturally to important crops such as rice, maize, barley and wheat in a persistent manner by the planthoppers, Laodelphax striatellus, Unkanodes sapporona and Unkanodes albifascia. Insect vector transmission tests are the basis for identifying viral incidence, evaluating the resistance of varieties and selecting resistance sources for rice and maize breeding. A simple, rapid and reliable method is described by which virus‐free small brown planthoppers (L. striatellus) acquired RBSDV from frozen infected rice leaves and transmitted it to healthy rice and maize plants. After feeding on frozen infected rice leaves, the planthoppers were tested by RT‐PCR for the presence of virus after 10, 15, and 22 days, respectively. The percentages of RBSDV‐containing insects were 0, 25 and 71.43% of L. striatellus fed on frozen infected rice leaves compared to 0, 28.25 and 71.43% of L. striatellus fed on fresh infected rice leaves, respectively. In transmission tests, three of eight rice seedlings (37.5%) and four of eight maize seedlings (50%) were inoculated by the planthoppers that had fed previously on frozen leaves and had allowed a 22 days latent period and showed typical disease symptoms. As a positive control, four of eight rice seedlings (50%) and four of six maize seedlings (66.67%) became infected. All rice and maize plants expressing disease symptoms were identified as virus‐positive by RT‐PCR. These results indicated that the planthoppers acquired RBSDV from frozen infected leaves and transmitted the virus to healthy plants.