A new mutation in the pufL gene responsible for the terbutryn resistance phenotype in Rubrivivax gelatinosus

A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy

The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.

The imidacloprid remediation, soil fertility enhancement and microbial community change in soil by Rhodopseudomonas capsulata using effluent as carbon source

The effects of Rhodopseudomonas capsulata (R. capsulata) in the treated effluent of soybean processing wastewater (SPW) on the remediation of imidacloprid in soil, soil fertility, and the microbial community structure in soil were studied. Compared with the control group, with the addition of effluent containing R. capsulata, imidacloprid was effectively removed, soil fertility was enhanced, and the microbial community structure was improved. Molecular analysis indicated that imidacloprid could exert induction effects on expression of cpm gene and regulation effects on the synthesis of cytochrome P450 monooxygenases (P450) by activating HKs gene in two-component system (TCS). For R. capsulata, this induction process required 1 day. The synthesis of P450 occurred 1 day after inoculation, because R. capsulata are a type of archaea and imidacloprid is an environmental stress. Before expression of the cpm gene and synthesis of P450, R. capsulata need a period of time to adapt to external imidacloprid stimulation. However, the lack of organic matter in the soil cannot sustain R. capsulata growth for more than 1 day. In four groups with added effluent, the remaining organic matter in the effluent provided a sufficient carbon source and energy for R. capsulata. Five days later, the microbial community structure was improved by R. capsulata in the soil. The new technique could be used to remediate imidacloprid, enhance soil fertility, treat SPW and realize the recycling and reuse of wastewater and R. capsulata cells.

Rhodopseudomonas sphaeroides treating mesosulfuron-methyl waste-water

The soybean processing wastewater (SPW) supplementation to facilitate the simultaneously treatment (SPW and mesosulfuron-methyl) of wastewater and production of biological substances by Rhodopseudomonas sphaeroides (R. sphaeroides) was discussed. Compared with the control group, with the addition of SPW, mesosulfuron-methyl was removed, and the yields of single-cell proteins, carotenoids, and bacteriochlorophyll were increased. In the 3 mg/L dose group, the mesosulfuron-methyl removal rate reached 97% after 5 days. Molecular analysis revealed that mesosulfuron-methyl exhibited induction effects on expression of the cpm gene and regulation effects on the synthesis of cytochrome P450 monooxygenases (P450) by activating HKs gene in TCS signal transduction pathway. For R. sphaeroides, this induction process required 1 day. The synthesis of P450 occurred 1 day after inoculation. Prior to expressing cpm gene and synthesizing P450, R. sphaeroides need a period of time to adapt to external mesosulfuron-methyl stimulation. However, the R. sphaeroides growth could not be maintained for more than 1 day due to the lack of organic matter in the raw wastewater. The SPW supplementation provided a sufficient carbon source in four groups with added SPW. After 5 days, R. sphaeroides became the dominant microflora in the wastewater. This new method could complete the treatment of mixed wastewater, the increased of biological substances output and the reuse of wastewater and R. sphaeroides cells as resources at the same time.

Photosynthetic bacteria-based technology is a potential alternative to meet sustainable wastewater treatment requirement?

A paradigm shift is underway in wastewater treatment from pollution removal to resource or energy recovery. However, conventional activated sludge (CAS) as the core technology of wastewater treatment is confronted with severe challenges on high energy consumption, sludge disposal and inevitable greenhouse gas emission, which are posing a serious impact on the current wastewater industry. It is urgent to find new alternative methods to remedy these defects. Photosynthetic bacteria (PSB) have flexible metabolic modes and high tolerance, which enhance the removal of nutrients, heavy metals and organic contaminants efficiency in different wastewater. The unique phototrophic growth of PSB breaks the restriction of nutrient metabolism in the CAS system. Recent studies have shown that PSB-based technologies can not only achieve the recovery of nutrient and energy, but also improve the degradation efficiency of refractory substances. If the application parameters can be determined, there will be great prospects and economic effects. This review summarizes the research breakthroughs and application promotion of PSB-based wastewater treatment technology in recent years. Comparing discussed the superiority and inferiority from the perspective of application range, performance differences and recovery possibility. Pathways involved in the nutrient substance and the corresponding influencing parameters are also described in detail. The mode of PSB biodegradation processes presented a promising alternative for new wastewater treatment scheme. In the future, more mechanical and model studies, deterministic operating parameters, revolutionary process design is need for large-scale industrial promotion of PSB-based wastewater treatment.

RETRACTED: Clothianidin wastewater treatment and the accumulation of high-value biochemical by Rhodopseudomonas spheroides

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Authors and the Editor-in-Chief. The paper is retracted because of a high level of duplication of "Rhodopseudomonas palustris wastewater treatment: cyhalofop-butyl removal, biochemicals production and mathematical model establishment. Bioresource. Tech. 2019, 282: 390-397 As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process. The first author, Pan Wu, takes full responsibility for these actions, a stance supported by Dalian Minzu University and Northeast Agricultural University, Harbin, where the research took place.

The biodegradation of carbaryl in soil with Rhodopseudomonas capsulata in wastewater treatment effluent

In this study, the effects of Rhodopseudomonas capsulata present in wastewater effluent on the biodegradation of carbaryl in soil and improvement of soil fertility were investigated. Compared to control treatment, carbaryl was removed efficiently and soil fertility was remediated with the addition of effluent containing R. capsulata. Molecular analysis revealed that carbaryl induced carbaryl hydrolase gene expression to synthesize carbaryl hydrolase through activating MAPKKKs, MAPKKs, MAPKs genes in MAPK signal transduction pathway. The induction and secretion of carbaryl hydrolase occur after one day in R. capsulata, which can be attributed to its characteristics as an ancient bacteria, which require acclimatization to carbaryl before gene induction. However, lack of organics in soil and control treatment could not maintain R. capsulata growth for over one day. The residual organics in the effluent provided sufficient carbon source and energy for R. capsulata under four effluent treatments. This new method resulted in the remediation of carbaryl pollution and improvement of soil fertility and soybean processing wastewater treatment simultaneously, as well as the reutilization of wastewater and R. capsulata as sludge. Meanwhile, the high-order non-linear mathematical model about carbaryl removal rate was established.

The removal of cyhalofop-butyl in soil by surplus Rhodopseudanonas palustris in wastewater purification

The biorestoration of cyhalofop-butyl and fertility in soil using Rhodopseudanonas palustris (R. palustris) in the treated wastewater were investigated in this research. Cyhalofop-butyl was not degraded under control group. The treated wastewater containing R. palustris degraded cyhalofop-butyl and remediated fertility. Interestingly, the cyhalofop-butyl-hydrolyzing carboxylesterase gene was expressed after inoculation 24 h. Subsequently, the cyhalofop-butyl-hydrolyzing carboxylesterase were synthesized to degrade cyhalofop-butyl. The cyhalofop-butyl started to be degraded after inoculation 24 h. The cyhalofop-butyl as stimulus signal induced cyhalofop-butyl-hydrolyzing carboxylesterase gene expression through signal transduction pathway. This process took 24 h for R. palustris as they were ancient bacteria. The residual organics in the wastewater provided sufficient carbon sources and energy for R. palustris under three dosage groups. The new method completed the remediation of cyhalofop-butyl pollution, the improvement of soil fertility and soybean processing wastewater treatment simultaneously, and realized the resource reutilization of wastewater and R. palustris as sludge.

Soybean processing wastewater supported the removal of propyzamide and biochemical accumulation from wastewater by Rhodopseudomonas capsulata

Simultaneous (SPW and propyzamide) wastewater treatment and the production of biochemicals by Rhodopseudomonas capsulata (R. capsulata) were investigated with supplement of soybean processing wastewater (SPW). Compared to control group, propyzamide was removed and biochemicals production were enhanced with the supplement of SPW. Propyzamide induced camH gene expression through activating MAPKKKs gene in MAPK signal transduction pathway. The induction of camH gene and CamH occurs after 1 day for R. capsulata. However, lack of organics in original wastewater did not maintain R. capsulata growth for over 1 day. The supplement of SPW provided sufficient carbon source for R. capsulata under three addition dosages. This new method resulted in the mixed (SPW and propyzamide) wastewater treatment and improvement of biochemicals simultaneously, as well as the realization of reutilization of wastewater and R. capsulata as sludge. Meanwhile, high-order nonlinear mathematical model of the relationship between propyzamide removal rate, Xt and Xt/r, was established.

Rhodopseudomonas palustris wastewater treatment: Cyhalofop-butyl removal, biochemicals production and mathematical model establishment

Simultaneous (SPW and cyhalofop-butyl) wastewater treatment and the production of biochemicals by Rhodopseudomonas palustris (R. palustris) was investigated with supplementation of soybean processing wastewater (SPW). Compared to control group, cyhalofop-butyl was removed and single cell protein, carotenoid, bacteriochlorophyll productions were enhanced with the supplementation of SPW. Cyhalofop-butyl removal reached 100% after 5 days under 4000 mg/L COD group. Cyhalofop-butyl induced chbH gene expression to synthesize cyhalofop-butyl-hydrolyzing carboxylesterase through activating MAPKKKs, MAPKKs, MAPKs genes in MAPK signal transduction pathway. The induction process took one day for R. palustris. However, lack of organics in original wastewater did not maintain R. palustris growth for over one day. The supplementation of SPW provided sufficient carbon source. This new method resulted in the mixed wastewater treatment and improvement of biochemicals simultaneously, as well as the realization of reutilization of R. palustris. High-order non-linear mathematical model of the relationship between R_chb, X_c, and X_t was established.

Identification of tenuazonic acid as a novel type of natural photosystem II inhibitor binding in Q(B)-site of Chlamydomonas reinhardtii

Tenuazonic acid (TeA) is a natural phytotoxin produced by Alternaria alternata, the causal agent of brown leaf spot disease of Eupatorium adenophorum. Results from chlorophyll fluorescence revealed TeA can block electron flow from Q(A) to Q(B) at photosystem II acceptor side. Based on studies with D1-mutants of Chlamydomonas reinhardtii, the No. 256 amino acid plays a key role in TeA binding to the Q(B)-niche. The results of competitive replacement with [(14)C]atrazine combined with JIP-test and D1-mutant showed that TeA should be considered as a new type of photosystem II inhibitor because it has a different binding behavior within Q(B)-niche from other known photosystem II inhibitors. Bioassay of TeA and its analogues indicated 3-acyl-5-alkyltetramic and even tetramic acid compounds may represent a new structural framework for photosynthetic inhibitors.

Interaction site for soluble cytochromes on the tetraheme cytochrome subunit bound to the bacterial photosynthetic reaction center mapped by site-directed mutagenesis

The crystallographic structure of the Blastochloris (formerly called Rhodopseudomonas) viridis tetraheme cytochrome subunit bound to the photosynthetic reaction center (RC) suggests that all four hemes are located close enough to the surface of the protein to accept electrons from soluble cytochrome c2. To identify experimentally the site of this reaction we prepared site-directed mutants of Rubrivivax gelatinosus RCs with surface charge substitutions in the bound cytochrome subunit and studied the kinetics of their reduction by soluble cytochromes (mitochondrial horse cytochrome c, Blc. viridis cytochrome c2, and Rvi. gelatinosus cytochrome c8). In comparison with the wild-type, the mutants E79K (glutamate-79 substituted by lysine), E93K (glutamate-93 substituted by lysine), and E85K (glutamate-85 substituted by lysine) located near the solvent-exposed edge of low-potential heme 1, the fourth heme from the special pair of bacteriochlorophyll, exhibited decreased second-order rate constants for the reaction between the tetraheme subunit and the soluble cytochromes. Double charge substitutions in this region: E79K/E85K (glutamate-79 and -85 both replaced by lysine) and E93K/E85K (glutamate-93 and -85 both replaced by lysine) appeared to show an additive inhibitory effect. Mutations in other charged regions did not alter the kinetics of electron transfer between bound and soluble cytochromes. In light of the available structural information on Blc. viridis RC, these results indicate that the cluster of acidic residues immediately surrounding the distal heme 1 of the RC-bound tetraheme subunit forms an electrostatically favorable binding site for soluble cytochromes. Thus, all four hemes in the subunit seem to be directly involved in the electron transfer toward the photo-oxidized special pair of bacteriochlorophyll. On the basis of these findings, a model is proposed for the hypothetical cytochrome c2-RC transient complex for Blc. viridis.

Photooxidative stress stimulates illegitimate recombination and mutability in carotenoid-less mutants of Rubrivivax gelatinosus

Carotenoids are essential to protection against photooxidative damage in photosynthetic and non-photosynthetic organisms. In a previous study, we reported the disruption of crtD and crtC carotenoid genes in the purple bacterium Rubrivivax gelatinosus, resulting in mutants that synthesized carotenoid intermediates. Here, carotenoid-less mutants have been constructed by disruption of the crtB gene. To study the biological role of carotenoids in photoprotection, the wild-type and the three carotenoid mutants were grown under different conditions. When exposed to photooxidative stress, only the carotenoid-less strains (crtB-) gave rise with a high frequency to four classes of mutants. In the first class, carotenoid biosynthesis was partially restored. The second class corresponded to photosynthetic-deficient mutants. The third class corresponded to mutants in which the LHI antenna level was decreased. In the fourth class, synthesis of the photosynthetic apparatus was inhibited only in aerobiosis. Molecular analyses indicated that the oxidative stress induced mutations and illegitimate recombination. Illegitimate recombination events produced either functional or non-functional chimeric genes. The R. gelatinosus crtB- strain could be very useful for studies of the SOS response and of illegitimate recombination induced by oxidants in bacteria.

Pleiotropic effects of puf interposon mutagenesis on carotenoid biosynthesis in Rubrivivax gelatinosus. A new gene organization in purple bacteria

Rubrivivax gelatinosus mutants affected in the carotenoid biosynthesis pathways were created by interposon mutagenesis within the puf operon. Genetic and biochemical analysis of several constructed mutants suggest that at least crtC is localized downstream of the puf operon and that it is cotranscribed with this operon. Sequence analysis confirmed the genetic data and showed the presence of crtD and crtC genes downstream of the puf operon, a localization different from that known for other purple bacteria. Inactivation of the crtD gene indicated that the two crt genes are cotranscribed and that they are involved not only in the hydroxyspheroidene biosynthesis pathway as in Rhodobacter sphaeroides and R. capsulatus, but also in the spirilloxanthin biosynthesis pathway. Carotenoid genes implicated in the spirilloxanthin biosynthesis pathway were thus identified for the first time. Furthermore, analysis of carotenoid synthesis in the mutants gave genetic evidence that crtD and crtC genes are cotranscribed with the puf operon using the oxygen-regulated puf promoter.

Development of gene transfer methods for Rubrivivax gelatinosus S1: construction, characterization and complementation of a puf operon deletion strain

Gene transfer systems were developed in Rubrivivax (Rx.) gelatinosus S1. First, a system for conjugative transfer of mobilizable plasmids from Escherichia coli to Rx. gelatinosus S1 was established. Secondly, optimal conditions for the transformation of Rx. gelatinosus S1 by electroporation were determined. A delta puf strain was constructed. Complementation with the puf operon from a wild-type strain cloned in a replicative plasmid restored photosynthetic growth. Two insertion strains were also selected. All the strains constructed were green, due to a change in carotenoid content. Characterization of these strains provides genetic evidence for a "superoperon" organization in this bacterium.