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De novo genes created in the plant mitochondrial genome have frequently been transferred into the nuclear genome via intergenomic gene transfer events. Therefore, plant mitochondria might be a source of de novo genes in the nuclear genome. However, the functions of de novo genes originating from mitochondria and the evolutionary fate remain unclear. Here, we revealed that an Arabidopsis thaliana specific small coding gene derived from the mitochondrial genome regulates floral transition. We previously identified 49 candidate de novo genes that induce abnormal morphological changes on overexpression. We focused on a candidate gene derived from the mitochondrial genome (sORF2146) that encodes 66 amino acids. Comparative genomic analyses indicated that the mitochondrial sORF2146 emerged in the Brassica lineage as a de novo gene. The nuclear sORF2146 emerged following an intergenomic gene transfer event in the A. thaliana after the divergence between Arabidopsis and Capsella. Although the nuclear and mitochondrial sORF2146 sequences are the same in A. thaliana, only the nuclear sORF2146 is transcribed. The nuclear sORF2146 product is localized in mitochondria, which may be associated with the pseudogenization of the mitochondrial sORF2146. To functionally characterize the nuclear sORF2146, we performed a transcriptomic analysis of transgenic plants overexpressing the nuclear sORF2146. Flowering transition-related genes were highly regulated in the transgenic plants. Subsequent phenotypic analyses demonstrated that the overexpression and knockdown of sORF2146 in transgenic plants resulted in delayed and early flowering, respectively. These findings suggest that a lineage-specific de novo gene derived from mitochondria has an important regulatory effect on floral transition.

Biopolymers are driving the plastic industry to the next generation of environmentally friendly bioproducts, considering green chemistry principles and contemporary economic concepts, such as environmental, social, and governance (ESG) criteria. Hence, microbial biopolymers arise in this context. Resulting from a natural carbon and energy storage process, polyhydroxyalkanoates are the raw material for a range of products based on plastic, with the advantage of being biodegradable in a short period of time. Discovering new biopolymers with different properties, carbon sources and PHA-related enzymes will facilitate market development as well as competition with petrochemical polymers. This work reports the experimental findings of PHA production and genomic data for two bacteria, Ralstonia pickettii and Aquitalea sp., isolated from a blackwater lake located in the ecological reserve of Tupe, Iranduba, AM, Brazil. They were able to produce PHB from carbon sources related to sugar, and R. pickettii also produced PHB from soybean oil and lignin derivatives. Whole-genome sequencing of these isolates enabled the identification of the genetic background to use other oxidizable carbon sources, such as lactic and malonic acids, amino acids, and lignin. Bacteria possibly capable of polyhydroxyalkanoate synthesis from lignin were investigated by genomics and chemistry of biomaterials. Aquitalea sp and Ralstonia pickettii isolated from a blackwater lake rich humic substances, showed great potential to be developed for this purpose. Canonical lignin degradation pathways, such as protocatechuate 4,5-dioxygenase-dependent pathway, CoA-dependent non-β-oxidation pathway of ferulic acid and β-ketoadipate pathway were mapped in their genomes. In addition, traces of P(3HB) were found when using vanillic and gallic acids as sole carbon source, which indicates that the downstream β-ketoadipate pathway is functional.

Increase in atmospheric carbon dioxide (CO2) has a significant effect on plant growth and development. To explore the elevated-CO2 response, we generated transcriptional profiles over a time course (2 h–14 days) of exposure to elevated CO2 in Arabidopsis thaliana. Genes related to photosynthesis were down-regulated and circadian rhythm-related genes were abnormally regulated in the early to middle phase of elevated CO2 exposure. To understand the novel mechanism of elevated CO2 signaling, we focused on 42 unknown small coding genes that showed differential expression patterns under elevated CO2 conditions. Four transgenic plants overexpressing the small coding gene exhibited a growth-defective phenotype under elevated CO2 but not under current CO2. Transcriptome analysis showed that circadian rhythm-related genes were commonly regulated in four transgenic plants. These circadian rhythm-related genes were transcribed in the dark when CO2 concentrations in the leaf was high. Taken together, our identified four small coding genes are likely to participate in elevated CO2 signaling to the circadian rhythm. Transcriptome analysis was performed under elevated CO2 condition in Arabidopsis thaliana. We identified small coding genes associated with signal molecules from elevated CO2 to circadian rhythm genes.

Hydrogen peroxide (H(2)O(2)) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H(2)O(2) in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H(2)O(2) application in Arabidopsis (Arabidopsis thaliana) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H(2)O(2) but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H(2)O(2) response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H(2)O(2) response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis.

Bacteria of the genus Bacillus have been investigated due to the ability that many species have of accumulating polyhydroxyalkanoates (PHA) via a wide variety of raw materials as their carbon source. Herein, we report the draft whole-genome sequence of the putative PHA-accumulating strain Bacillus paramycoides LB_RP2, isolated from an Amazonian river.

Increase in atmospheric carbon dioxide (CO

Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.

Polyhydroxyalkanoates (PHAs) are a group of natural biopolyesters that resemble petroleum-derived plastics in terms of physical properties but are less harmful biologically to the environment and humans. Most of the current PHA producers are heterotrophs, which require expensive feeding materials and thus contribute to the high price of PHAs. Marine photosynthetic bacteria are promising alternative microbial cell factories for cost-effective, carbon neutral and sustainable production of PHAs. In this study,Rhodovulum sulfidophilum, a marine photosynthetic purple nonsulfur bacterium with a high metabolic versatility, was evaluated for cell growth and PHA production under the influence of various media components found in previous studies. We evaluated iron, using ferric citrate, as another essential factor for cell growth and efficient PHA production and confirmed that PHA production inR. sulfidophilumwas growth-associated under microaerobic and photoheterotrophic conditions. In fact, a subtle amount of iron (1 to 2 μM) was sufficient to promote rapid cell growth and biomass accumulation, as well as a high PHA yield during the logarithmic phase. However, an excess amount of iron did not enhance the growth rate or PHA productivity. Thus, we successfully confirmed that an optimum concentration of iron, an essential nutrient, promotes cell growth inR. sulfidophilumand also enhances PHA utilization.

The plant growth-promoting fungus (PGPF), Penicillium simplicissimum GP17-2 (GP17-2), induces systemic resistance against Pseudomonas syringae pv. tomato DC3000 (Pst) in Arabidopsis thaliana. The molecular mechanisms underlying induced systemic resistance (ISR) by GP17-2 were investigated in the present study. Microscopic observations revealed that stomatal reopening by Pst was restricted by elicitation with the culture filtrate (CF) from GP17-2. A gene expression analysis of MYB44, which enhances abscisic acid signaling and consequently closes stomata, revealed that the gene was activated by CF. CF-elicited myb44 mutant plants failed to restrict stomatal reopening and showed lower resistance to Pst than wild-type plants. These results indicate that stomatal resistance by GP17-2 is mediated by the gene activation of MYB44. We herein revealed that the MYB44-mediated prevention of penetration through the stomata is one of the components responsible for GP17-2-elicited ISR.

The plant growth-promoting fungus (PGPF), Penicillium simplicissimum GP17-2 (GP17-2), induces systemic resistance against Pseudomonas syringae pv. tomato DC3000 (Pst) in Arabidopsis thaliana. The molecular mechanisms underlying induced systemic resistance (ISR) by GP17-2 were investigated in the present study. Microscopic observations revealed that stomatal reopening by Pst was restricted by elicitation with the culture filtrate (CF) from GP17-2. A gene expression analysis of MYB44, which enhances abscisic acid signaling and consequently closes stomata, revealed that the gene was activated by CF. CF-elicited myb44 mutant plants failed to restrict stomatal reopening and showed lower resistance to Pst than wild-type plants. These results indicate that stomatal resistance by GP17-2 is mediated by the gene activation of MYB44. We herein revealed that the MYB44-mediated prevention of penetration through the stomata is one of the components responsible for GP17-2-elicited ISR.

Brassinosteroids are plant steroid hormones that regulate plant organs and chloroplast development. The detailed molecular mechanism for plant development by BR signaling is yet to be revealed, and many points regarding the relationship between BR signaling and chloroplast development remain unknown. We identify here the dominant mutant Brz-insensitive-pale green3-1D (bpg3-1D) from the Arabidopsis FOX lines that show reduced sensitivity to the chlorophyll accumulation promoted by the BR biosynthesis inhibitor, Brassinazole (Brz), in the light. BPG3 encodes a novel chloroplast protein that is evolutionally conserved in bacteria, algae, and higher plants. The expression of BPG3 was induced by light and Brz. The inhibition of electron transport in photosystem II of the chloroplasts was detected in bpg3-1D. These results suggest that BPG3 played an important role in regulating photosynthesis in the chloroplast under BR signaling.

Mutant resources are indispensable for the characterization of the functions of genes. There are two types of mutants, loss-of-function and gain-of-function mutants. Recently, we have developed a novel system in plants that uses a gain-of-function approach and is named as the FOX (full-length cDNA overexpressor gene) hunting system. In this system, Arabidopsis full-length cDNAs (fl-cDNAs) are randomly over-expressed under the control of the cauliflower mosaic virus (CaMV) 35S promoter in Arabidopsis plants. These transgenic plants, or Arabidopsis FOX lines, possess ectopically expressed fl-cDNAs in their genome. Chemical genomics is a newly emerging field that connects chemical biology with genomes. Since each FOX line expresses an excess amount of the protein from the transgene it can be resistant or hypersensitive to bioactive chemicals when the protein is the target for the chemical. In this protocol, we describe the procedure for identification of the fl-cDNAs responsible for the target of the chemical or for the signal transduction pathway involving the chemical.

Mutant resources are indispensable for the characterization of the functions of genes. There are two types of mutants, loss-of-function and gain-of-function mutants. Recently, we have developed a novel system in plants that uses a gain-of-function approach and is named as the FOX (full-length cDNA overexpressor gene) hunting system. In this system, Arabidopsis full-length cDNAs (fl-cDNAs) are randomly over-expressed under the control of the cauliflower mosaic virus (CaMV) 35S promoter in Arabidopsis plants. These transgenic plants, or Arabidopsis FOX lines, possess ectopically expressed fl-cDNAs in their genome. Chemical genomics is a newly emerging field that connects chemical biology with genomes. Since each FOX line expresses an excess amount of the protein from the transgene it can be resistant or hypersensitive to bioactive chemicals when the protein is the target for the chemical. In this protocol, we describe the procedure for identification of the fl-cDNAs responsible for the target of the chemical or for the signal transduction pathway involving the chemical.

Mutant populations are indispensable tools for investigating plant gene functions. Gain-of-function technology is one of the approaches used for the systematic production of mutant resources and activation tagging is a well-established method to generate gain-of-function mutants in plants. As an alternative approach for the systematic generation of a gain-of-function mutant population, we developed the Full-length cDNA OvereXpressor (FOX)-hunting system in which full-length cDNAs (fl-cDNAs) are overexpressed in plants to quickly identify candidate genes. The FOX-hunting system was used for high-throughput analysis of rice (Oryza sativa) genes heterologously expressed in Arabidopsis thaliana (rice FOX Arabidopsis lines). A large screening to identify and characterize rice genes with rice FOX Arabidopsis lines revealed that one of the isolated genes, BROAD-SPECTRUM RESISTANCE 1 (BSR1) conferred multiple or broad-spectrum disease resistance in both a dicotyledonous and monocotyledonous plant. We found that expression of rice fl-cDNAs without a homolog in Arabidopsis affected morphological traits. In addition, overexpression of homologous genes of rice and Arabidopsis led to a similar phenotype. Thus, we conclude that the FOX-hunting system is an excellent heterologous system and offers a new tool with which to explore gene function in rice.

RNA-binding proteins (RBPs) play an important role in plant host-microbe interactions. In this study, we show that the plant RBP known as FPA, which regulates 3'-end mRNA polyadenylation, negatively regulates basal resistance to bacterial pathogen Pseudomonas syringae in Arabidopsis. A custom microarray analysis reveals that flg22, a peptide derived from bacterial flagellins, induces expression of alternatively polyadenylated isoforms of mRNA encoding the defence-related transcriptional repressor ETHYLENE RESPONSE FACTOR 4 (ERF4), which is regulated by FPA. Flg22 induces expression of a novel isoform of ERF4 that lacks the ERF-associated amphiphilic repression (EAR) motif, while FPA inhibits this induction. The EAR-lacking isoform of ERF4 acts as a transcriptional activator in vivo and suppresses the flg22-dependent reactive oxygen species burst. We propose that FPA controls use of proximal polyadenylation sites of ERF4, which quantitatively limit the defence response output.