Random mutagenesis in a plant viral genome using a DNA repair-deficient mutator Escherichia coli strain

Construction and biological characterization of an Agrobacterium-mediated infectious cDNA of squash mosaic virus

Squash mosaic virus (SqMV), a member of the species Squash mosaic virus in the genus Comovirus (family Comoviridae), is an important seed-borne virus that causes serious economic losses in cucurbit crops. Here, we constructed infectious cDNA clones of SqMV genomic RNAs (RNA1 and RNA2) under the control of the cauliflower mosaic virus (CaMV) 35S promoter by Gibson assembly. The infectious cDNA clones of SqMV could infect zucchini squash (Cucurbita pepo) plants systemically by agrobacterium-mediated inoculation. The virus progeny from the infectious clones showed no difference from the wild type in terms of pathogenicity and symptom induction. It could be mechanically transmitted to zucchini squash (Cucurbita pepo), pumpkin (Cucurbita moschata), cucumber (Cucumis sativus), and muskmelon (Cucumis melo) but not watermelon (Citrullus lanatus) or Nicotiana benthamiana. This is the first report of construction of a SqMV infection clone and will facilitate the investigation of viral pathogenesis and host interactions.

Improved activity of the Cel5A endoglucanase in Saccharomyces cerevisiae deletion mutants defective in oxidative stress defense mechanisms

OBJECTIVES

Developing a Saccharomyces cerevisiae system for optimizing the expression of recombinant eukaryotic proteins.

RESULTS

Two deletion mutants, which were hypersensitive to H2O2, were obtained by knocking out CTT1 and SOD2, respectively. The mutation rate of the mutants was up to over 4000 times of the spontaneous mutation rate when treated with H2O2. Endoglucanase Cel5A was used as a model enzyme to evaluate the system for improving the expression of the recombinant protein. Sixteen mutants of the RDKY3615 (ctt1∆) transformant and seven mutants of the RDKY3615 (sod2∆) transformant had significantly high Cel5A activity, while none mutants of the RDKY3615 transformant had significantly high enzyme activity.

CONCLUSION

The combination of deletion mutagenesis and H2O2 treatment greatly accelerate the generation of genetic variants and will be a useful tool in improving the heterologous expression in S. cerevisiae.

Technologies of directed protein evolution in vivo

Directed evolution of proteins for improved or modified functionality is an important branch of modern biotechnology. It has traditionally been performed using various in vitro methods, but more recently, methods of in vivo artificial evolution come into play. In this review, we discuss and compare prokaryotic and eukaryotic-based systems of directed protein evolution in vivo, highlighting their benefits and current limitations and focusing on the biotechnological potential of vertebrate immune cells for the generation of protein diversity by means of the immunoglobulin diversification machinery.

Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment

Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.

A single silent substitution in the genome of Apple stem grooving virus causes symptom attenuation

Among randomly mutagenized clones derived from an infectious cDNA copy of genomic RNA of Apple stem grooving virus (ASGV), we previously identified a clone, pRM21, whose in vitro transcript (ASGV-RM21) does not induce any symptoms characteristic of the original (wild-type) cDNA clone (ASGV-wt) in several host plants. Interestingly, ASGV-RM21 has only a single, translationally silent nucleotide substitution, U to C, at nucleotide 4646 of the viral genome within open reading frame (ORF) 1. Here, we characterize and verify this unprecedented silent-mutation-induced attenuation of symptoms in infected plants. Northern and Western blot analyses showed that less ASGV-RM21 accumulates in host plants than ASGV-wt. In addition, two more silent substitutions, U to A and U to G, constructed by site-directed mutagenesis at the same nucleotide (4646), also induced attenuated symptoms. This is the first report that a single silent substitution attenuates virus-infection symptoms and implicates a novel determinant of disease symptom severity.