Shigeru Kuwata

Point mutations in the coat protein of cucumber mosaic virus affect symptom expression and virion accumulation in tobacco

We examined the correlation of the amino acid at position 129 in the coat protein (CP) of cucumber mosaic virus (CMV) with the phenotype of the viral pathology in tobacco by using CP mutants in which several amino acid substitutions had been introduced. An exchange between Ser129 in CMV-Y, a chlorosis-inducing strain, and Pro129 of CMV-O, a green-mosaic-inducing strain, reciprocally altered the phenotypes of those virus strains on tobacco. Replacement of either Ser129 in CMV-Y or Pro129 in CMV-O with a Leu, as is found in a chlorosis-inducing strain, CMV-M, resulted in veinal necrosis. Furthermore, we created mutants that have a Phe or a Gly at position 129. Two Phe129 mutants induced necrotic lesions on the inoculated leaves, and a Gly129 mutant induced green mosaic symptoms. In inoculated protoplasts, the mutant viruses and the wild-type virus all replicated RNA well, and accumulated CP; however, infection with the Leu129 and Phe129 mutants yielded few virions. The Phe129 mutants lacked the capacity to move systemically in tobacco; by 2 weeks post-inoculation, the Phe129 mutants occasionally gave rise to revertants that elicited chlorosis, green mosaic or veinal necrosis. Sequence analysis revealed that one had reverted to the parental Y strain, and the others had additional single amino acid changes (positions 138, 144 or 147). We suggest that amino acids at specific sites affect the whole structure of the CP and affect virus assembly, virus transport and symptom expression.

Tailor-made TALEN system for highly efficient targeted gene replacement in the rice blast fungus.

CRISPR/Cas‐derived RNA‐guided nucleases (RGNs) that can generate DNA double‐strand breaks (DSBs) at a specific sequence are widely used for targeted genome editing by induction of DSB repair in many organisms. The CRISPR/Cas system consists of two components: a single Cas9 nuclease and a single‐guide RNA (sgRNA). Therefore, the system for constructing RGNs is simple and efficient, but the utilization of RGNs in filamentous fungi has not been validated. In this study, we established the CRISPR/Cas system in the model filamentous fungus, Pyricularia oryzae, using Cas9 that was codon‐optimized for filamentous fungi, and the endogenous RNA polymerase (RNAP) III U6 promoter and a RNAP II fungal promoter for the expression of the sgRNA. We further demonstrated that RGNs could recognize the desired sequences and edit endogenous genes through homologous recombination‐mediated targeted gene replacement with high efficiency. Our system will open the way for the development of various CRISPR/Cas‐based applications in filamentous fungi. Biotechnol. Bioeng. 2015;112: 2543–2549.

Infection Dynamics in Viral Spread and Interference Under the Synergism Between Cucumber mosaic virus and Turnip mosaic virus

Mixed infection of Cucumber mosaic virus (CMV) and Turnip mosaic virus (TuMV) induced more severe symptoms on Nicotiana benthamiana than single infection. To dissect the relationships between spatial infection patterns and the 2b protein (2b) of CMV in single or mixed infections, the CMV vectors expressing enhanced green fluorescent or Discosoma sp. red fluorescent proteins (EGFP [EG] or DsRed2 [Ds], respectively were constructed from the same wild-type CMV-Y and used for inoculation onto N. benthamiana. CMV2-A1 vector (C2-A1 [A1]) has a functional 2b while CMV-H1 vector (C2-H1 [H1]) is 2b deficient. As we expected from the 2b function as an RNA silencing suppressor (RSS), in a single infection, A1Ds retained a high level of accumulation at initial infection sites and showed extensive fluorescence in upper, noninoculated leaves, whereas H1Ds disappeared rapidly at initial infection sites and could not spread efficiently in upper, noninoculated leaf tissues. In various mixed infections, we found two phenomena providing novel insights into the relationships among RSS, viral synergism, and interference. First, H1Ds could not spread efficiently from vasculature into nonvascular tissues with or without TuMV, suggesting that RNA silencing was not involved in CMV unloading from vasculature. These results indicated that 2b could promote CMV to unload from vasculature into nonvascular tissues, and that this 2b function might be independent of its RSS activity. Second, we detected spatial interference (local interference) between A1Ds and A1EG in mixed infection with TuMV, between A1Ds (or H1Ds) and TuMV, and between H1Ds and H1EG. This observation suggested that local interference between two viruses was established even in the synergism between CMV and TuMV and, again, RNA silencing did not seem to contribute greatly to this phenomenon.

Tailor-made TALEN system for highly efficient targeted gene replacement in the rice blast fungus: Tailor-Made TALENs for the Rice Blast Fungus

Genetic manipulation is key to unraveling gene functions and creating genetically modified strains of microbial organisms. Recently, engineered nucleases that can generate DNA double‐strand breaks (DSBs) at a specific site in the desired locus within genome are utilized in a rapidly developing genome editing technology via DSBs repair. However, the use of engineered nucleases in filamentous fungi has not been validated. In this study, we demonstrated that tailor‐made transcriptional activator‐like effector nucleases (TALENs) system, Platinum–Fungal TALENs (PtFg TALENs), could improve the efficiency of homologous recombination‐mediated targeted gene replacement by up to 100% in the rice blast fungus Pyricularia oryzae. This high‐efficiency PtFg TALEN has great potential for basic and applied biological applications in filamentous fungi. Biotechnol. Bioeng. 2015;112: 1335–1342.

Competition between wild-type virus and a reassortant from subgroups I and II of CMV and activation of antiviral responses in cowpea

Summary.To investigate the interactions between RNA3 and RNA4 from subgroups I and II in mixed infections, accumulation of CMV RNA were analyzed. In the mixed inoculation assays with CMV-LE (LE, subgroup I) and a reassortant LLm consisting of RNA1 and RNA2 from LE, and RNA3 from CMV-m2 (m2, subgroup II), LE RNA3 and RNA4 could systemically spread in the plants, whereas those of m2 could not. Furthermore, accumulation of virus short RNA and a cowpea-encoded RNA-directed RNA polymerase gene (VuRdRP1) mRNA were found in the plants, suggesting that VIGS and/or distinct antiviral responses (was) were activated by infection with CMV.

Site‐specific DNA double‐strand break generated by I‐SceI endonuclease enhances ectopic homologous recombination in Pyricularia oryzae

To evaluate the contribution of DNA double-strand breaks (DSBs) to somatic homologous recombination (HR) in Pyricularia oryzae, we established a novel detection/selection system of DSBs-mediated ectopic HR. This system consists of donor and recipient nonfunctional yellow fluorescent protein (YFP)/blasticidin S deaminase (BSD) fusion genes and the yeast endonuclease I-SceI gene as a recipient-specific DSB inducer. The system enables to detect and select ectopic HR events by the restoration of YFP fluorescence and blasticidin S resistance. The transformed lines with donor and recipient showed low frequencies of endogenous ectopic HR (> 2.1%). Compared with spontaneous HR, c. 20-fold increases in HR and absolute frequency of HR as high as 40% were obtained by integration of I-SceI gene, indicating that I-SceI-mediated DSB was efficiently repaired via ectopic HR. Furthermore, to validate the impact of DSB on targeted gene replacement (TGR), the transformed lines with a recipient gene were transfected with an exogenous donor plasmid in combination with the DSB inducer. TGR events were not observed without the DSB inducer, whereas hundreds of colonies resulting from TGR events were obtained with the DSB inducer. These results clearly demonstrated that the introduction of site-specific DSB promotes ectopic HR repair in P. oryzae.

Molecular analysis of coat protein coding region of tobacco stunt virus shows that it is a strain of Lettuce big-vein virus in the genus Varicosavirus

Summary.To evaluate the relationship between tobacco stunt virus (TStV) and Lettuce big-vein virus (LBVV), we determined nucleotide sequences of the coat protein (CP) coding region of five TStV and three LBVV isolates and compared them with those of one Japanese and four Spanish isolates of LBVV. CP coding regions were identical in size and the nucleotide and amino acid sequence identities between TStV and LBVV were 95.6–96.5% and 97.2–98.7%, respectively. Phylogenetic analysis of nucleotide sequences indicated that TStV was very closely related to LBVV and a strain of LBVV rather than a distinct species.

Lentiavidins: Novel avidin-like proteins with low isoelectric points from shiitake mushroom (Lentinula edodes).

A biotin-binding protein with a low isoelectric point (pI), which minimizes electrostatic non-specific binding to substances other than biotin, is potentially valuable. To obtain such a protein, we screened hundreds of mushrooms, and detected strong biotin-binding activity in the fruit bodies of Lentinula edodes, shiitake mushroom. Two cDNAs, each encoding a protein of 152 amino acids, termed lentiavidin 1 and lentiavidin 2 were cloned from L. edodes. The proteins shared sequence identities of 27%-49% with other biotin-binding proteins, and many residues that directly associate with biotin in streptavidin were conserved in lentiavidins. The pI values of lentiavidin 1 and lentiavidin 2 were 3.9 and 4.4, respectively; the former is the lowest pI of the known biotin-binding proteins. Lentiavidin 1 was expressed as a tetrameric protein with a molecular mass of 60 kDa in an insect cell-free expression system and showed biotin-binding activity. Lentiavidin 1, with its pI of 3.9, has a potential for broad applications as a novel biotin-binding protein.

Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae

To provide experimental evidence that somatic homologous recombination (HR) is involved in the instability and diversification of the avirulence gene Avr-Pita in Pyricularia oryzae, we generated a dysfunctional Avr-Pita homolog and integrated it into strain Hoku-1 containing Avr-Pita. In the transformants, the occurrence of somatic HR events between Avr-Pita and the dysfunctional homolog was confirmed by PCR–RFLP. Germlings from conidia from the HR-positive transformants had lost the avirulence function, which enabled it to infect rice cultivar Yashiromochi containing the corresponding resistant gene Pi-ta. These results suggested that genetic mutation caused by somatic HR is one of the mechanisms responsible for virulence diversity.

Plant viral translation strategies and disease resistance conferred by recessive host genes

Viruses are obligate intracellular parasites that can multiply only inside living cells. Upon entry of the virus into a host cell, the capsid must be disassembled, and viral RNAs translated into proteins, thereby enabling the virus to replicate efficiently by suppressing host defense responses. Generally, the genome sizes of plant viruses are smaller than those of animal viruses, and their genomes code for 4–10 viral proteins. Therefore, the majority of viral proteins are multifunctional. Because of their simple composition, plant virus genomes and their encoded proteins have been extensively studied. The establishment of infectious RNA transcription systems for positive-strand RNA viruses has enabled extensive analysis of the functions of viral proteins by reverse genetic approaches. To analyze the functions of viral proteins, I have constructed infectious RNA transcription systems for several positive-strand RNA plant viruses including cucumber mosaic virus (CMV), tobacco mosaic virus (TMV), tobacco streak virus (TSV), and alfalfa mosaic virus (AMV). While dealing with infectious transcription systems for TSV and AMV, I realized that translation initiation of viral proteins has very important implications in the life cycle of the positivestrand RNA viruses. Implications of translation initiation of viral proteins in the virus life cycle