Estimation of biophysical characteristics for <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis> pigment mutants with an M-PEA-2 fluorometer

Light green pigment mutants with a reduced chlorophyll b content were constructed in the microalga Chlamydomonas reinhardtii Dangeard. A simultaneous recording of the induction curves for prompt and delayed fluorescence and the redox state of P700 in the microsecond range with a M-PEA-2 fluorometer revealed decreases in the quantum yield of electron transport in PS2 (φE₀) and the performance index (PI_ABS) and increases in the quantum efficiency of energy dissipation (φD₀) and ΔpH-dependent nonphotochemical quenching (qE and NPQ). The light-dependence curves of the fluorescence parameters confirmed a decrease in the coefficient of maximum utilization of light energy (α) for the mutants. However, the mutants showed an adequate rate of electron transport at a medium light intensity under steady-state conditions. The mutations did not directly affect the oxidation reactions of the PS1 pigment (P700) and the decrease in delayed fluorescence. Experience in using the mutants to test polluted waters of Kazakhstan confirmed that the mutants are promising for use in biomonitoring for mutagens.     

Dot1 and Set2 histone methylases control the spontaneous and UV-induced mutagenesis levels in the <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> yeasts

In the Saccharomyces cerevisiae yeasts, the DOT1 gene product provides methylation of lysine 79 (K79) of histone H3 and the SET2 gene product provides the methylation of lysine 36 (K36) of the same histone. We determined that the dot1 and set2 mutants suppress the UV-induced mutagenesis to an equally high degree. The dot1 mutation demonstrated statistically higher sensitivity to the low doses of MMC than the wild type strain. The analysis of the interaction between the dot1 and rad52 mutations revealed a considerable level of spontaneous cell death in the double dot1 rad52 mutant. We observed strong suppression of the gamma-induced mutagenesis in the set2 mutant. We determined that the dot1 and set2 mutations decrease the spontaneous mutagenesis rate in both single and double mutants. The epistatic interaction between the dot1 and set2 mutations and almost similar sensitivity of the corresponding mutants to the different types of DNA damage allow one to conclude that both genes are involved in the control of the same DNA repair pathways, the homologous-recombination-based and the postreplicative DNA repair.     

Effect of chromate ions on marine microalgae <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis>

Effect of chromate ions on the culture of a marine diatom Phaeodactylum tricornutum was studied using an M-PEA-2 fluorimeter, which carries out simultaneous measurement of fluorescence induction and redox transformations of the P₇₀₀ pigment within a millisecond range. Chromate ions were shown to inhibit electron transport in PS II and decrease the rate of Q_А reduction. This results in decreased values of the quantum yield of electron transport in PS II (?_Eo) and performance index (PI _ABS), lower rates of P700 reduction, and increased energy (DI0/RC) and ΔpH-dependent nonphotochemical quenching (q _E ). Emergence of the slow component of P₇₀₀ reduction was observed, indicating the activation of cyclic transport in the presence of chromate. Performance index (PI _ABS), which was the most sensitive parameter, may be recommended for detection of chromate ions at early stages of their toxic action. The fluorescence parameter F _O is promising application in biotesting to assess the algal growth rates.     

Evaluation of microbial globin promoters for oxygen-limited processes using <Emphasis Type="Italic">Escherichia coli</Emphasis>

Oxygen-responsive promoters can be useful for synthetic biology applications, however, information on their characteristics is still limited. Here, we characterized a group of heterologous microaerobic globin promoters in Escherichia coli. Globin promoters from Bacillus subtilis, Campylobacter jejuni, Deinococcus radiodurans, Streptomyces coelicolor, Salmonella typhi and Vitreoscilla stercoraria were used to express the FMN-binding fluorescent protein (FbFP), which is a non-oxygen dependent marker. FbFP fluorescence was monitored online in cultures at maximum oxygen transfer capacities (OTR_max) of 7 and 11 mmol L^?1 h^?1. Different FbFP fluorescence intensities were observed and the OTR_max affected the induction level and specific fluorescence emission rate (the product of the specific fluorescence intensity multiplied by the specific growth rate) of all promoters. The promoter from S. typhi displayed the highest fluorescence emission yields (the quotient of the fluorescence intensity divided by the scattered light intensity at every time-point) and rate, and together with the promoters from D. radiodurans and S. coelicolor, the highest induction ratios. These results show the potential of diverse heterologous globin promoters for oxygen-limited processes using E. coli.     

The role of thiol redox systems in the response of <Emphasis Type="Italic">Escherichia coli</Emphasis> to far-UV irradiation

Escherichia coli mutants deficient in glutathione (gshA), glutaredoxin (grxA), thioredoxin (trxA), and thioredoxin reductase (trxB) synthesis were studied with respect to their resistance to far-UV (UV₂₅₄) exposure. The trxA, trxB, and grxA mutants subjected to a short-term UV exposure were found to be more resistant to UV irradiation than the parent cells. Under the same conditions, the trxA and trxB mutants demonstrated a high level of induction of the sulA gene, a component of the SOS regulon. The mutagenic effect of long-term UV exposure of all the mutants with redox deficiencies was more pronounced than in the case of the parent strain, and the trxA and trxB mutants were found to be the least viable microorganisms. Pretreatment of the cells with low concentrations of the thiol-oxidizing agent diamide enhanced the sulA gene expression; however, high concentrations of diamide inhibited sulA expression. The data obtained indicate that the thiol redox systems of E. coli are involved in its response to far-UV irradiation.     

Quorum sensing systems of regulation,synthesis of phenazine antibiotics,and antifungal activity in rhizospheric bacterium <Emphasis Type="Italic">pseudomonas chlororaphis</Emphasis> 449

Strain Pseudomonas chlororaphis 449, an antagonist of a broad spectrum of phytopathogenic microorganisms isolated from the maize rhizosphere, was shown to produce three phenazine antibiotics: phenazine-1-carboxylic acid (PCA), 2-hydroxylphenazine-1-carboxylic acid (2-OH-PCA), and 2-hydroxylphenazine (2-OH-PHZ). Two Quorum Sensing (QS) systems of regulation were identified: Phz/R and CsaI/R. Genes phzI and csaI were cloned and sequenced. Cells of strain 449 synthesize at least three types of AHL: N-butanoyl-L-homoserine lactone (C₄-AHL), N-hexanoyl-L-homoserine lactone (C₆-AHL), and N-(3-oxo-hexanoyl)-L-homoserine lactone (30C₆-AHL). Transposon mutagenesis was used to generate mutants of strain 449 deficient in synthesis of phenazines, which carried inactivated phzA and phzB genes of the phenazine operon and gene phzO. Mutations phzA ^? and phzB ^? caused a drastic reduction in the antagonistic activity of bacteria toward phytopathogenic fungi. Both mutants lost the ability to protect cucumber and leguminous plants against phytopathogenic fungi Rhizoctonia solani and Sclerotinia sclerotiorum. These results suggest a significant role of phenazines in the antagonistic activity of P. chlororaphis 449.     

The use of parameters of chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence induction to evaluate the state of plants under anthropogenic load

The physiological state of the leaves of the small-leaved linden (Tilia cordata), silver birch (Betula pendula), and northern white cedar (Thuja occidentalis) under urban conditions was assessed via recording the kinetics of chlorophyll under fluorescence induction. Different sensitivities of the plants to adverse growing conditions were revealed. The most sensitive parameters of the fluorescence JIP test, viz., PI _ABS , F _V/F ₀, and F _V/F _M, were identified as indicators of the physiological state of the urban phytocoenosis. Recommendations for the application of the method for monitoring studies are presented.     

Single point mutations enhance activity of <Emphasis Type="Italic">cis</Emphasis>-epoxysuccinate hydrolase

Objectives

To enhance activity of cis-epoxysuccinate hydrolase from Klebsiella sp. BK-58 for converting cis-epoxysuccinate to tartrate.

Results

By semi-saturation mutagenesis, all the mutants of the six important conserved residues almost completely lost activity. Then random mutation by error-prone PCR and high throughput screening were further performed to screen higher activity enzyme. We obtained a positive mutant F10D after screening 6000 mutations. Saturation mutagenesis on residues Phe10 showed that most of mutants exhibited higher activity than the wild-type, and the highest mutant was F10Q with activity of 812 U mg^?1 (k _cat /K _m , 9.8 ± 0.1 mM^?1 s^?1), which was 230 % higher than that of wild-type enzyme 355 U mg^?1 (k _cat /K _m , 5.3 ± 0.1 mM^?1 s^?1). However, the thermostability of the mutant F10Q slightly decreased.

Conclusions

The catalytic activity of a cis-epoxysuccinate hydrolase was efficient improved by a single mutation F10Q and Phe10 might play an important role in the catalysis.

     

Analysis of the expression of the <Emphasis Type="Italic">Rhodobacter sphaeroides lexA</Emphasis> gene

The regulation of the Rhodobacter sphaeroides lexA gene has been analyzed using both gel-mobility experiments and lacZ gene fusions. PCR-mediated mutagenesis demonstrated that the second GAAC motif in the sequence GAACN₇GAACN₇GAAC located upstream of the R. sphaeroides lexA gene is absolutely necessary for its DNA damage-mediated induction. Moreover, mutagenesis of either the first or the third GAAC motif in this sequence reduced, but did not abolish, the inducibility of the R. sphaeroides lexA gene. A R. sphaeroides lexA-defective (Def) mutant has also been constructed by replacing the active lexA gene with an inactivated gene copy constructed in vitro. Crude extracts of the R. sphaeroides lexA(Def) strain are unable to form any protein-DNA complex when added to the wild-type lexA promoter of R. sphaeroides. Likewise, the R. sphaeroides lexA(Def) cells constitutively express the recA and lexA genes. All these data clearly indicate that the lexA gene product is the negative regulator of the R. sphaeroides SOS response. Furthermore, the morphology, growth and viability of R. sphaeroides lexA(Def) cultures do not show any significant change relative to those of the wild-type strain. Hence, R. sphaeroides is so far the only bacterial species whose viability is known not to be affected by the presence of a lexA(Def) mutation.     

Isolating and confirming the <Emphasis Type="Italic">MuDR</Emphasis>-inserted flanking sequences of maize

MuDR exhibits the highest transposition activity and insertional mutagenesis frequency in Mutator (Mu) family. If we isolate the MuDR-insertion-specific flanking sequences (MuDRFs), it will be crucial for using Mu element-mediated mutants. The MuDR-TAIL-PCR system was constructed and optimized using a combination of MuDR-TIR-nested specific primers and 12 arbitrary degenerate (AD) primers, modified reaction system and procedure and mutant DNA templates of 87 genotypes from M₂ or М_2:3 families created by crossing the W22::Mu line (active MuDR donor parent) from the UniformMu population with the Zong31 (Z31) line (recipient parent). Here 129 different MuDRFs were acquired by MuDR-TAIL-PCR, accounting for 86.60% of the total mutant-specific agarose gel bands. In addition, we confirmed the authenticity of the non-redundant flanking sequence amplifications. The amplified non-redundant flanking sequences accounted for 65.12% of the total MuDRFs, and 88.00% of the non-redundant MuDRFs were inserted inside the genes. These results show that the MuDR-TAIL-PCR system that we developed can be used for specifically isolating MuDRFs.     

Altered somatic mutation level and DNA repair gene expression in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> exposed to ultraviolet C,salt, and cadmium stresses

It is known that somatic mutations arising during animal growth and ageing contribute to the development of neurodegenerative and other animal diseases. For plants, several studies showed that small-scale somatic DNA mutations accumulated during Arabidopsis life cycle. However, there is a lack of data on the influence of environmental stresses on somatic DNA mutagenesis in plants. In this study, we analyzed the effects of ultraviolet C (UV-C) irradiation, high soil salinity, and cadmium (CdI₃) stresses on the level of small-scale somatic DNA mutations in Arabidopsis thaliana. The number of DNA mutations was examined in the Actin2 3′UTR (Actin-U1), ITS1-5.8rRNA-ITS2 (ITS), and ribulose-1,5-biphosphate carboxylase/oxygenase (rbcL) DNA regions. We found that somatic mutation levels considerably increased in CdI₃-treated Arabidopsis plants, while the mutation levels declined in the UV-C- and NaCl-treated A. thaliana. Cadmium is a mutagen that is known to inhibit DNA repair processes. The detected stress-induced alterations in somatic DNA mutation levels were accompanied by markedly increased expression of base excision repair genes (AtARP, AtDME, AtDML2, AtDML3, AtMBD4, AtROS, AtUNG, and AtZDP), nucleotide excision repair genes (AtDDB1a, AtRad4, and AtRad23a), mismatch repair genes (AtMSH2, AtMSH3, and AtMSH7), and photoreactivation genes (AtUVR2, AtUVR3). Thus, the results demonstrated that UV-C, high soil salinity, and cadmium stresses influence both the level of DNA mutations and expression of DNA repair genes. Salt- and UV-induced activation of DNA repair genes could contribute to the stress-induced decrease in somatic mutation level.     

<Emphasis Type="Italic">PiggyBac</Emphasis> transposon-mediated mutagenesis and application in yeast <Emphasis Type="Italic">Komagataella phaffii</Emphasis>

Objective

Around one-fourth of the Komagataella phaffii genes encode hypothetical proteins with unknown functions. However, lack of powerful tools for genetic screening in K. phaffii significantly limits the functional analysis of these unknown genes. Transposon mutagenesis has been utilized as an insertional mutagenesis tool in many other organisms and would be extremely valuable if it could be applied in K. phaffii.

Results

In this study, we investigated in K. phaffii the transposition activity and efficiency of piggyBac (PB) transposon, a DNA transposon from the cabbage looper moth Trichoplusia ni through the integrated-plasmid system. We also designed a binary-plasmid system which could generate stable mutants. Finally we evaluated the quality of this mutagenesis system by a simple screening for functional genes involved in K. phaffii carbon catabolite repression.

Conclusions

Our results demonstrate that PB-mediated mutagenesis could be a feasible and useful tool for functional gene screening in K. phaffii.

     

Acclimation of shade-tolerant and light-resistant <Emphasis Type="Italic">Tradescantia</Emphasis> species to growth light: chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence,electron transport,and xanthophyll content

In this study, we have compared the photosynthetic characteristics of two contrasting species of Tradescantia plants, T. fluminensis (shade-tolerant species), and T. sillamontana (light-resistant species), grown under the low light (LL, 50–125 µmol photons m^?2 s^?1) or high light (HL, 875–1000 µmol photons m^?2 s^?1) conditions during their entire growth period. For monitoring the functional state of photosynthetic apparatus (PSA), we measured chlorophyll (Chl) a emission fluorescence spectra and kinetics of light-induced changes in the heights of fluorescence peaks at 685 and 740 nm (F ₆₈₅ and F ₇₄₀). We also compared the light-induced oxidation of P₇₀₀ and assayed the composition of carotenoids in Tradescantia leaves grown under the LL and HL conditions. The analyses of slow induction of Chl a fluorescence (SIF) uncovered different traits in the LL- and HL-grown plants of ecologically contrasting Tradescantia species, which may have potential ecophysiological significance with respect to their tolerance to HL stress. The fluorometry and EPR studies of induction events in chloroplasts in situ demonstrated that acclimation of both Tradescantia species to HL conditions promoted faster responses of their PSA as compared to LL-grown plants. Acclimation of both species to HL also caused marked changes in the leaf anatomy and carotenoid composition (an increase in Violaxanthin?+?Antheraxantin?+?Zeaxanthin and Lutein pools), suggesting enhanced photoprotective capacity of the carotenoids in the plants grown in nature under high irradiance. Collectively, the results of the present work suggest that the mechanisms of long-term PSA photoprotection in Tradescantia are based predominantly on the light-induced remodeling of pigment-protein complexes in chloroplasts.     

The <Emphasis Type="Italic">APX4</Emphasis> locus regulates seed vigor and seedling growth in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

The amino acid sequence of APX4 is similar to other ascorbate peroxidases (APXs), a group of proteins that protect plants from oxidative damage by transferring electrons from ascorbate to detoxify peroxides. In this study, we characterized two apx4 mutant alleles. Translational fusions with GFP indicated APX4 localizes to chloroplasts. Both apx4 mutant alleles formed chlorotic cotyledons with significantly reduced chlorophyll a, chlorophyll b and lutein. Given the homology of APX to ROS-scavenging proteins, this result is consistent with APX4 protecting seedling photosystems from oxidation. The growth of apx4 seedlings was stunted early in seedling development. In addition, APX4 altered seed quality by affecting seed coat formation. While apx4 seed development appeared normal, the seed coat was darker and more permeable than the wild type. In addition, accelerated aging tests showed that apx4 seeds were more sensitive to environmental stress than the wild-type seeds. If APX4 affects seed pigment biosynthesis or reduction, the seed coat color and permeability phenotypes are explained. apx4 mutants had cotyledon chlorosis, increased H₂O₂ accumulation, and reduced soluble APX activity in seedlings. These results indicate that APX4 is involved in the ROS-scavenging process in chloroplasts.     

The effect of galling aphids feeding on photosynthesis photochemistry of elm trees (<Emphasis Type="Italic">Ulmus</Emphasis> sp.)

Changes of chlorophyll (Chl) a fluorescence and photosynthetic pigment contents were analysed in galled leaves (visibly damaged and undamaged parts) and intact leaves. The values of minimal fluorescence of the dark-adapted state, maximal quantum yield of PSII photochemistry, effective quantum yield of PSII photochemical conversion, and photochemical quenching coefficient decreased in Ulmus pumila L. leaves galled by Tetraneura ulmi (L.) and in U. glabra Huds. galled by Eriosoma ulmi (L.). Colopha compressa (Koch.) feeding affected these parameters only in damaged parts of U. laevis Pall. galled leaves. The increasing number of T. ulmi galls progressively decreased photosynthetic performance. In gall tissues of all analysed aphid species, the lowest photosynthetic pigment content was found, indicating that the photosynthetic capacity must have been low in galls. Significant reduction of Chl and carotenoid contents were observed in damaged and undamaged portions of galled leaves only in the case of T. ulmi feeding.     

Revealing physiological and genetic properties of a dominant maize dwarf <Emphasis Type="Italic">Dwarf11</Emphasis> (<Emphasis Type="Italic">D11</Emphasis>) by integrative analysis

Plant height is an important agronomic trait involved in lodging resistance and harvest index. The identification and characterization of mutants that are defective in plant height have implications for trait improvement in breeding programs. Two dominant maize dwarf mutants D8 and D9 have been well-characterized. Here, we report the characterization of a dominant maize dwarf mutant Dwarf11 (D11). Dwarf stature of D11 was mainly attributed to the inhibition of longitudinal cell elongation. The levels of bioactive GA₃ were significantly lower in D11. Contrarily, D8 mutant accumulates markedly higher levels of GA₃. The expression of GA biosynthetic and catabolic genes was dramatically decreased in D11. Expression variations of d8 and d9 genes were not observed in D11 mutant. Moreover, genetic suppressors of D11 were identified in inbred line Chang 7-2. Integrated omics data indicated that D11 is a novel dominant maize dwarf. The ultimate D11 gene cloning and its regulatory network elucidation may strengthen our understanding of the genetic basis of plant architecture and provide cues for breeding of crops with plant height ideotypes.     

Enhancing the efficiency of the <Emphasis Type="Italic">Pichia pastoris AOX1</Emphasis> promoter via the synthetic positive feedback circuit of transcription factor Mxr1

Background

The methanol-regulated AOX1 promoter (P_AOX1) is the most widely used promoter in the production of recombinant proteins in the methylotrophic yeast Pichia pastoris. However, as the tight regulation and methanol dependence of P_AOX1 restricts its application, it is necessary to develop a flexible induction system to avoid the problems of methanol without losing the advantages of P_AOX1. The availability of synthetic biology tools enables researchers to reprogram the cellular behaviour of P. pastoris to achieve this goal.

Results

The characteristics of P_AOX1 are highly related to the expression profile of methanol expression regulator 1 (Mxr1). In this study, we applied a biologically inspired strategy to reprogram regulatory networks in P. pastoris. A reprogrammed P. pastoris was constructed by inserting a synthetic positive feedback circuit of Mxr1 driven by a weak AOX2 promoter (P_AOX2). This novel approach enhanced P_AOX1 efficiency by providing extra Mxr1 and generated switchable Mxr1 expression to allow P_AOX1 to be induced under glycerol starvation or carbon-free conditions. Additionally, the inhibitory effect of glycerol on P_AOX1 was retained because the synthetic circuit was not activated in response to glycerol. Using green fluorescent protein as a demonstration, this reprogrammed P. pastoris strain displayed stronger fluorescence intensity than non-reprogrammed cells under both methanol induction and glycerol starvation. Moreover, with single-chain variable fragment (scFv) as the model protein, increases in extracellular scFv productivity of 98 and 269% were observed in Mxr1-reprogrammed cells under methanol induction and glycerol starvation, respectively, compared to productivity in non-reprogrammed cells under methanol induction.

Conclusions

We successfully demonstrate that the synthetic positive feedback circuit of Mxr1 enhances recombinant protein production efficiency in P. pastoris and create a methanol-free induction system to eliminate the potential risks of methanol.

     

Effect of high light intensity on the photosynthetic apparatus of two hybrid lines of <Emphasis Type="Italic">Paulownia</Emphasis> grown on soils with different salinity

The objective of this investigation was to evaluate the simultaneous action of light stress and salinity. Pulse amplitude modulated chlorophyll fluorescence, P₇₀₀ redox state, and pigment analysis were used to assess the impact of high light intensity on Paulownia tomentosa × fortunei and Paulownia elongata × elongata grown on soils with different salinity. It was found that light stress reduced the amount of pigments and the efficiency of photochemical energy conversion, inhibited the maximum and the effective quantum yields of PSII photochemistry, decreased photochemical quenching and photosynthetic rate. Data also showed influence on the primary quinone acceptor (Q_A) reoxidation, which led to the restriction of the electron flow from Q_A to plastoquinone and stimulation of the cyclic electron flow. The possible reasons for the increased effects of the light stress under conditions of high salt concentration in soil for Paulownia tomentosa × fortunei are discussed.