Unraveling Fe(II)-oxidizing mechanisms in a facultative Fe(II) oxidizer Sideroxydans lithotrophicus ES-1 via culturing, transcriptomics, and RT-qPCR

Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or thiosulfate oxidation, in contrast to most other neutrophilic Fe(II)-oxidizing bacteria (FeOB) isolates. This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with RT-qPCR. We explored the long-term gene expression response at different growth phases (over days-week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II) even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO 2 is an important electron sink for Fe(II) oxidation. Importance Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual amongst neutrophilic FeOB isolates as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment, and suggest a multi-gene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.

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179. PURIFICATION AND CHARACTERISATION OF MOUSE TESTICULAR MACROPHAGES: GENE EXPRESSION RESPONSE TO LIPOPOLYSACCHARIDE ACTIVATION INDICATES AN IMMUNOSUPPRESSIVE PHENOTYPE

Reproduction Fertility and Development ◽

10.1071/srb10abs179 ◽

2010 ◽

Vol 22 (9) ◽

pp. 97

Author(s):

W. R. Winnall ◽

J. Gould ◽

J. A. Muir ◽

P. Hertzog ◽

M. P. Hedger

Keyword(s):

Gene Expression ◽

Microarray Analysis ◽

Inflammatory Mediators ◽

Inflammatory Cytokine ◽

Transforming Growth Factor ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Gene Expression Response ◽

Anti Inflammatory ◽

Testicular Macrophages

Studies on rat testicular macrophages (TMs) have indicated that these cells play an important role in testis function by supporting the immunosuppressive environment that protects developing germ cells and by responding to pathogens. By comparison, mouse TMs are essentially uncharacterised due to difficulties in isolating sufficient cells for study. We have established a technique for isolating 95% pure TMs from adult mice by differential adherence. Mouse TMs were cultured for 3h with saline, 10 or 100 ng/mL lipopolysaccharide (LPS) and compared with resident peritoneal macrophages (PMs) and bone marrow-derived macrophages (BMMs). Expression of inflammatory regulators was determined using real-time Q-PCR and AgilentTM microarray analysis. Microarray analysis indicated that each macrophage type displayed very distinct gene expression profiles. There were 526 genes uniquely expressed in TMs at basal levels compared with the other macrophages and 268 genes uniquely expressed by TMs after LPS treatment. Q-PCR determined that LPS induced expression of the anti-inflammatory cytokine interleukin (IL)-10 in each of the macrophage types, with BMMs the strongest responders. LPS stimulated IL-10 mRNA approximately 100-fold in TMs, but only 20-fold in PMs. The anti-inflammatory transforming growth factor-β1 was not significantly induced at this time-point in any macrophage type. In terms of pro-inflammatory mediators, the TM response to LPS was always lower compared to the BMMs. Compared to PMs, the responses of TMs were similar for the hallmark pro-inflammatory cytokine tumour necrosis factor- a, but 40% less for IL-1β. TMs were also deficient in production of IL-6 and cyclooxygenase-2 and IL-12. TMs were therefore relatively strong responders to LPS in terms of IL-10, but weak responders in terms of pro-inflammatory mediators, indicating an immunosuppressive phenotype. The isolation and gene measurement methods established in this study will allow us to use knockout and transgenic mouse models to determine the role for TMs in testicular inflammation/fibrosis models.

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Timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae).

10.1101/2021.11.10.468112 ◽

2021 ◽

Author(s):

Karolina Heyduk ◽

Edward McAssey ◽

James Leebens-Mack

Keyword(s):

Gene Expression ◽

Carbon Fixation ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Transcriptional Response ◽

Time Of Day ◽

Temporal Separation ◽

Genes Encoding ◽

Cam Species ◽

Cam Photosynthesis

CAM photosynthesis has evolved repeatedly across the plant tree of life, yet our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. CAM is furthermore thought to be closely linked to the circadian clock in order to achieve temporal separation of carboxylation and sugar production. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well-watered and drought-stressed treatments. We further assessed gene expression and molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. In contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms, and evidence of positive selection in PPC genes implicates mutations that may have facilitated the recruitment for CAM function early in the evolutionary history of the Agavoideae. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.

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Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1804971115 ◽

2018 ◽

Vol 115 (30) ◽

pp. 7831-7836 ◽

Cited By ~ 29

Author(s):

Yukio Kurihara ◽

Yuko Makita ◽

Mika Kawashima ◽

Tomoya Fujita ◽

Shintaro Iwasaki ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Transcript Abundance ◽

Initial Growth ◽

Transcription Start ◽

Transcription Start Sites ◽

Genome Wide ◽

Nonsense Mediated Mrna Decay ◽

Inducible Genes

Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH, major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5, accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.

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