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Omics score: 27

RNA-seq of Clostridium acetobutylicum ATCC 55025, histidine kinase Cac3319 and Cac0437 inactivated strains.

ABSTRACT: The goal of this experiment is compare gene expression profiles between C. acetobutylicum ATCC 55025, histidine kinase cac3319 and cac0437 inactivated strains to determine the pleiotropic and distinctive functions of histidine kinases on cell differentiation and cellular metabolism. Samples for total RNA extraction were collected from fermentation broth at acidogenic phase (8 h) and solventogenic phase (16 h)

INSTRUMENT(S): RNeasy Mini Kit, Eppendorf Centrifuge, ABI PCR Instruments, Illumina HiSeq 2000

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Guangqing Du Chuang Xue

PROVIDER: E-MTAB-7341 | ArrayExpress | 2019-05-01

SECONDARY ACCESSION(S): ERP111682

REPOSITORIES: ArrayExpress, ENA

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			Action	DRS
	E-MTAB-7341.idf.txt	Idf
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	E-MTAB-7341.sdrf.txt	Txt

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RNA-seq of Clostridium acetobutylicum ATCC 55025, histidine kinase Cac3319 and Cac0437 inactivated strains.

Project description:The goal of this experiment is compare gene expression profiles between C. acetobutylicum ATCC 55025, histidine kinase cac3319 and cac0437 inactivated strains to determine the pleiotropic and distinctive functions of histidine kinases on cell differentiation and cellular metabolism. Samples for total RNA extraction were collected from fermentation broth at acidogenic phase (8 h) and solventogenic phase (16 h)

2019-05-01 | E-MTAB-7341 | BioStudies

Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature.

Project description:In this study the root transcriptome profiles of young seedlings (5 days after germination at 23C) of two tomato species differing in cold tolerance were analysed and compared after a subsequent treatment for 3 days at 23 or 15C by RNAseq. Aim was to elucidate molecular mechanisms underlying root development associated with suboptimal-temperature tolerance during early seedling establishment.

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WGS histidine overproducers

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Metabolic Engineering of Histidine Kinases in Clostridium beijerinckii for Enhanced Butanol Production.

Project description:Clostridium beijerinckii, a promising industrial microorganism for butanol production, suffers from low butanol titer and lack of high-efficiency genetical engineering toolkit. A few histidine kinases (HKs) responsible for Spo0A phosphorylation have been demonstrated as functionally important components in regulating butanol biosynthesis in solventogenic clostridia such as C. acetobutylicum, but no study about HKs has been conducted in C. beijerinckii. In this study, six annotated but uncharacterized candidate HK genes sharing partial homologies (no less than 30%) with those in C. acetobutylicum were selected based on sequence alignment. The encoding region of these HK genes were deleted with CRISPR-Cas9n-based genome editing technology. The deletion of cbei2073 and cbei4484 resulted in significant change in butanol biosynthesis, with butanol production increased by 40.8 and 17.3% (13.8 g/L and 11.5 g/L vs. 9.8 g/L), respectively, compared to the wild-type. Faster butanol production rates were observed, with butanol productivity greatly increased by 40.0 and 20.0%, respectively, indicating these two HKs are important in regulating cellular metabolism in C. beijerinckii. In addition, the sporulation frequencies of two HKs inactivated strains decreased by 96.9 and 77.4%, respectively. The other four HK-deletion (including cbei2087, cbei2435, cbei4925, and cbei1553) mutant strains showed few phenotypic changes compared with the wild-type. This study demonstrated the role of HKs on sporulation and solventogenesis in C. beijerinckii, and provided a novel engineering strategy of HKs for improving metabolite production. The hyper-butanol-producing strains generated in this study have great potentials in industrial biobutanol production.

2020-01-01 | S-EPMC7098912 | BioStudies

Histidine-dependent protein methylation is required for compartmentalization of CTP synthase

Project description:CTP synthase (CTPS) forms compartmentalized filaments in response to substrate availability and environmental nutrient status. However, the physiological role of filaments and mechanisms for filament assembly are not well understood. Here, we provide evidence that CTPS forms filaments in response to histidine influx during glutamine starvation. CTPS protein levels remained stable in the presence of histidine during nutrient deprivation, followed by rapid cell growth following nutrient replenishment. Tetramer conformation-based filament formation restricted CTPS enzyme activity duringnutrient deprivation. Furthermore, we demonstrated that filament formation controlled at two levels. Starvation stress/glutamine deficiency activates the GCN2/ATF4/MTHFD2 axis to accelerate the folate cycle in mitochondria for energy homeostasis. In addition, histidine promotes re-methylation of homocysteine by donating one-carbon to the cytosolic folate cycle. CTPS filament formation induced by histidine-mediated methylation maybe a strategy usedby cancer cells to maintain homeostasis and ensure a growth advantage in adverse environments. Overall design: Cell culture in different medium (DMEM, EBSS and EBSS+Histidine) for 4 h, with two independent experiment

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Studying the effects of endogenous and exogenous histidine supplementation on Pichia pastoris cultured in YPA

Project description:A histidine prototrophic strain achieves A600 three-four fold higher than a histidine auxotroph when cultured in nutrient rich media YPA, which is abundant in amino acids. This retaded growth of histidine auxotroph in YPA can also be rescued by supplementing media with exogenous histidine. Here, we aim to study the transcriptomic changes associated with culturing of histidine auxotroph and prototroph in YPA and also the effects of histidine addition to the culture medium of histidine auxotroph. Overall design: Wild type cells were cultured in nutrient rich medium containing yeast extract, peptone and acetate as a carbon source (YPA), alone or supplemented with 650 uM histidiene. Cells were harvested after 24 hours followed by RNA preparation using QIAGEN RNEASY Mini Kit which was then subjected to RNA-SEQ.

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RNA-seq of mutant Mycobacterium neoaurum producing steroid intermediates compared with wild-type strain

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