2-Stage PAC and syngas into L-malate
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB72504 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12652200_1.fastq.gz | Fastqsanger.gz | |||
| ERR12652200_2.fastq.gz | Fastqsanger.gz | |||
| ERR12652201_1.fastq.gz | Fastqsanger.gz | |||
| ERR12652201_2.fastq.gz | Fastqsanger.gz | |||
| ERR12652202_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Understanding the mechanism of malate accumulation in plants is beneficial for both plant nutrient and human health. However, little is known regarding regulation of malate accumulation in horticulture plants such as tomato. The goals of this study are to investigate potential regulation network of Al-Activated Malate Transporter 9 (ALMT9) which is the major locus responsible for the variation in fruit malate concentration observed in cultivared tomato. Methods: The transcriptomes of fruit at ripening stage from CK and SlALMT9 overexpressing line1 were evaluated using single-ended sequencing of Illumina HiSeq 2500. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by tophat and edgeR software. Results: Among 1,887 differentially expressed genes, some structural genes involved in sugar and organic acid metabolism were differently expressed in SlALMT9 overexpressing line, which partially coincide with changes of sugar and organic acid concentration. PR genes was also altered in the OX lines, in agreement with previous study that tomato fruit malate is involved in pathogen infection. Three members of malate transporters, MATE (multidrug and toxin efflux), were up-regulated (SlMATE5 and 6) or down-regulated (SlMATE9) . Besides, three sugar transport proteins and four vacuole membrane or plasma membrane proteins were up-regulated in OX line Conclusions: Using RNA-seq analysis, 1,887 differentially expressed genes was revealed. Among them, several genes related to sugar and organic acid metabolism and transport, pathogen resistances were identified. This transcriptome study provides insight into the regulatory mechanism of fruit malate accumulation and the effect of the SlALMT9 to primary metabolism.
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Project description:Clostridium ljungdahlii derives energy by acetogenesis as a lithotrophic pathway and as part of various organotrophic pathways. Its recently sequenced genome has made it possible to discover changes in gene expression that occur in different growth modes, from which strategies for biofuel production may be developed. C. ljungdahlii was grown with fructose as an organoheterotrophic substrate and also lithoautotrophically, either on syngas or with H2 as the electron donor and CO2 as the electron acceptor. RNA extracted from all three conditions was analyzed by hybridization to a microarray, and gene expression was compared quantitatively by RNA-Seq of C. ljungdahlii grown with fructose and with H2 and CO2. Results. Strongly upregulated (> 10-fold, p < 0.05) genes with both syngas and H2/CO2 encode enzymes that degrade aspartate and arginine through the urea cycle to control the release of ammonia from amino acids. Numerous genes for uptake and degradation of peptides and amino acids, response to sulfur starvation, and molybdopterin-dependent pathways were also significantly (> 2-fold, p < 0.05) upregulated, along with three potentially NADPH-producing pathways for which the key metabolites are (S)-malate, ornithine and 6-phospho-D-gluconate. Upregulation of genes implicated in quorum sensing, sporulation and cell wall remodeling suggests a global and multicellular response to lithoautotrophic conditions. With syngas, (R)-lactate dehydrogenase and associated electron transfer flavoproteins were upregulated, representing a route of electron transfer from ferredoxin to NAD that is independent of the proton-translocating Rnf complex. With H2/CO2, a flavodoxin and histidine biosynthesis enzymes were upregulated. Genes for degradation of purine bases entering the cell by facilitated diffusion were upregulated in lithotrophic cells, whereas genes for degradation of adenine or adenosine derivatives entering by active transport were significantly (2-fold, p < 0.05) downregulated. The most downregulated genes, after those specific to fructose metabolism, encode enzymes of pyrimidine and purine biosynthesis, arginine fermentation to ornithine, threonine biosynthesis and phosphate uptake. Genes for biogenesis of an intracytoplasmic microcompartment were downregulated, within which (S)-1,2-propanediol dehydratase and other enzymes may dispose of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several redox-active proteins, both cytoplasmic and membrane-associated, and predicted cell surface proteins were identified as differentially regulated. Conclusion. The transcriptomic profiles of C. ljungdahlii in lithoautotrophic and organoheterotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide the production of biofuels and commodity chemicals with this species.
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Project description:Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.
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