Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide

Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO2 under both aerobic and anaerobic conditions. High solubility of CO2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO2 as compared to N2 and O2 limited conditions. While both CO2 and N2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO2. Interestingly, signal transduction was uniquely regulated under CO2 condition, where up-regulated genes (STE3, MSB2, WSC3, STE12 and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO2 sensing and CO2-induced metabolisms in yeast. Our study identifies CO2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.

Transcriptomics and metabolomics of engineered Synechococcus elongatus during photomixotrophic growth

Background

Converting carbon dioxide (CO₂) into value-added chemicals using engineered cyanobacteria is a promising strategy to tackle the global warming and energy shortage issues. However, most cyanobacteria are autotrophic and use CO₂ as a sole carbon source, which makes it hard to compete with heterotrophic hosts in either growth or productivity. One strategy to overcome this bottleneck is to introduce sugar utilization pathways to enable photomixotrophic growth with CO₂ and sugar (e.g., glucose and xylose). Advances in engineering mixotrophic cyanobacteria have been obtained, while a systematic interrogation of these engineered strains is missing. This work aimed to fill the gap at omics level.

Results

We first constructed two engineered Synechococcus elongatus YQ2-gal and YQ3-xyl capable of utilizing glucose and xylose, respectively. To investigate the metabolic mechanism, transcriptomic and metabolomic analysis were then performed in the engineered photomixotrophic strains YQ2-gal and YQ3-xyl. Transcriptome and metabolome of wild-type S. elongatus were set as baselines. Increased abundance of metabolites in glycolysis or pentose phosphate pathway indicated that efficient sugar utilization significantly enhanced carbon flux in S. elongatus as expected. However, carbon flux was redirected in strain YQ2-gal as more flowed into fatty acids biosynthesis but less into amino acids. In strain YQ3-xyl, more carbon flux was directed into synthesis of sucrose, glucosamine and acetaldehyde, while less into fatty acids and amino acids. Moreover, photosynthesis and bicarbonate transport could be affected by upregulated genes, while nitrogen transport and assimilation were regulated by less transcript abundance of related genes in strain YQ3-xyl with utilization of xylose.

Conclusions

Our work identified metabolic mechanism in engineered S. elongatus during photomixotrophic growth, where regulations of fatty acids metabolism, photosynthesis, bicarbonate transport, nitrogen assimilation and transport are dependent on different sugar utilization. Since photomixotrophic cyanobacteria is regarded as a promising cell factory for bioproduction, this comprehensive understanding of metabolic mechanism of engineered S. elongatus during photomixotrophic growth would shed light on the engineering of more efficient and controllable bioproduction systems based on this potential chassis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01760-1.

Low-level concentrations of aminoglycoside antibiotics induce the aggregation of cyanobacteria

The interactions between antibiotics and microorganisms have attracted enormous research attentions. In this study, we investigated the effects of two typical aminoglycoside antibiotics on the aggregation of the model cyanobacterium, Synechococcus elongatus, and the dominating strain in algal blooms, Microcystis aeruginosa, via the analysis of zeta potentials, hydrophobicity, and extracellular polymeric substances (EPS) secretion. The results showed that low-level antibiotics promoted the aggregation of S. elongatus and M. aeruginosa by 40 and 18% under 0.10 and 0.02 μg/mL of kanamycin, respectively, which was mainly attributed to the combined effects of increased zeta potentials and the ratio between extracellular proteins and polysaccharides. Tobramycin exerted similar effects. Additionally, we discovered that at low pH (pH 5) and ionic strength (1 mM Na⁺ and 2 mM Mg²⁺), the inducing effects of antibiotics would be even larger than those with higher pH and ionic strength. As aggregation is important to cyanobacteria in either the basic physiology of biofilm formation or the algal bloom, our study demonstrated that low-level antibiotics exert ecological impacts via interfered aggregation. We believe this study will shed light on the mechanisms underlying antibiotic-induced biofilm formation and help with the evaluation of the environmental and ecological risks of antibiotics and other emerging pollutants.

Synthetic Whole-Cell Biodevices for Targeted Degradation of Antibiotics

Synthetic biology enables infinite possibilities in biotechnology via employing genetic modules. However, not many researches have explored the potentials of synthetic biology in environmental bioprocesses. In this study, we introduced a genetic module harboring the codon-optimized tetracycline degrading gene, tetX.co, into the model host, Escherichia coli, and generated a prototypal whole-cell biodevice for the degradation of a target antibiotic. Our results suggested that E. coli with the tetX.co-module driven by either the P_J23119 or P_BAD promoters conferred resistance up to 50 μg/mL of tetracycline and degrades over 95% of tetracycline within 24 h. The detoxification ability of tetX was further verified in conditioned media by typical E. coli K-12 and B strains as well as Shewanella oneidensis. Our strategy demonstrated the feasibility of introducing genetic modules into model hosts to enable environmental functions, and this work will inspire more environmental innovations through synthetic biological devices.

Micelle-mediated transport disturbance providing extracellular strategy for alleviating n-butanol stress on Escherichia coli

One barrier inhibiting further progress in biofuel production is the toxicity of biofuels towards their producers. It is promising to apply gene-based intracellular techniques to engineer better strains with higher organic solvent tolerance. These methods are, however, complex. In the present study, we developed a simple, manageable, and commercial extracellular prototypal strategy to alleviate n-butanol (n-BuOH) stress on Escherichia coli via a micelle-mediated transport disturbance. When the concentration of sodium dodecyl sulfate, a typical anionic surfactant, is high enough to form micelles, n-BuOH will be trapped into/onto the micelles, and the negative charge prevents the n-BuOH from approaching the cells. Our study provides an extracellular strategy to relieve the stress from n-BuOH, and it also exhibits a new angle to advance microbial factories through extracellular routines.

Ecological insights into low-level antibiotics interfered biofilms of Synechococcus elongatus

The ecological impacts of low-level kanamycin onS. elongatushave been investigated through combined biofilm formation and transcriptional analysis.

Extracellular polymeric substances protect Escherichia coli from organic solvents

The protective roles of extracellular polymeric substances againstn-butanol have been investigated and determined.

Sentinel lymphadenectomy for breast cancer in a community managed care setting

PURPOSE

To evaluate the feasibility, accuracy, and reproducibility of intraoperative lymphatic mapping and sentinel lymphadenectomy (IOLM/SL) in the staging of breast cancer patients in a community managed care setting.

PATIENTS AND METHODS

One hundred forty-five patients with primary breast cancer were prospectively studied over a 26-month period. They underwent vital dye injection at their primary breast cancer site. Lymphatic channels were traced to the sentinel lymph node, which was excised, serially sectioned, and examined. A level I and II axillary lymph node dissection and definitive breast surgery were then performed.

RESULTS

Sentinel nodes were identified in 103 of 145 procedures (71.0%). Sentinel and nonsentinel lymph nodes were concordant in 100 of 103 cases (97.1%). Three patients (9.7%) had falsely negative sentinel nodes; there were none in the last 80 patients. Of 28 positive sentinel nodes, 12 (42.9%) represented the only tumor-containing node within the axilla. Sentinel nodes were significantly more likely to contain tumor than nonsentinel nodes (33/50, 66.0% vs 54/467, 11.6%, P < 0.0001). IOLM/SL identified more micrometastases (< 2 mm) than standard axillary lymph node dissection (13/33, 39.6% vs 4/177, 2.2%, P < 0.001). Nine of 42 patients (21.4%) whose sentinel node could not be identified had five or more nodal metastases. Two of six patients with presumed Tis primaries had nodal metastases.

DISCUSSION

IOLM/SL accurately identifies the sentinel lymph node(s) most likely to contain metastatic disease. A procedural learning curve was present. An unsuccessful IOLM/SL was a risk factor for considerable nodal metastases. IOLM/SL with a tumor-free sentinel node may obviate a formal axillary lymph node dissection. The technique was feasible, economical, and reproducible within the context of a community managed care facility, while not placing exacting demands on operating room, pathology, or nuclear medicine personnel.

Outpatient definitive breast cancer surgery

We attempted to show that surgical treatment of breast cancer, including axillary lymph node dissection with or without concomitant partial mastectomy (ALND), simple mastectomy (SM), and modified radical mastectomy (MRM) can be performed safely in an outpatient setting. The records of 100 consecutive women undergoing definitive breast cancer surgery by the authors between August 1994 and July 1996 were retrospectively reviewed. Average age was 54 +/- 10 years. Fifty patients were discharged the day of surgery, 44 were hospitalized, and 6 remained 2 or more days postoperatively. Outpatients were more likely to have undergone ALND or SM (42 versus 23 procedures) and more often completed surgery in the morning (36 versus 12); P < 0.05. Eight patients of 35 with MRM were discharged the same day. One patient was readmitted with a wound infection. There were no major complications or deaths. Ninety-four per cent of patients were discharged within 23 hours of surgery; half were discharged the same day. No complications occurred in outpatients, and there were no readmissions. For patients admitted overnight, no complications were detected during the overnight hospital stay. In conclusion, breast cancer surgery, from ALND to SM or MRM, can be safely and comfortably performed on an outpatient basis.

Segmental mastectomy and tamoxifen alone provide adequate locoregional control of breast cancer in elderly women

We wished to determine whether tamoxifen and local excision without breast radiation or axillary lymph node dissection provides adequate local and regional control of breast cancer in elderly women. The records of 36 women with breast cancer who were more than 70 years old and were treated only with tamoxifen and local excision from January 1985 to July 1996 were retrospectively reviewed. These patients had refused, or were considered too ill for, standard therapy. The mean follow-up was 44.1 months. Twenty-two (61%) were alive without disease, and six (17%) died of unrelated causes, without recurrence. Two (6%) were alive with metastasis, and five (14%) died with metastasis. One patient developed a breast recurrence, which was reexcised. A second patient developed metastasis and axillary recurrence, which was treated with modified radical mastectomy. Pathologic grade, tumor size, and estrogen receptor and margin status were not predictive of recurrence. In conclusion, despite the omission of breast radiation and axillary dissection, there were only two locoregional recurrences, and both were easily treated surgically. In this select group of patients, local excision and tamoxifen provided adequate locoregional control of breast cancer in elderly women.

Superoxide dismutase and allopurinol improve survival in an animal model of hemorrhagic shock

We studied the efficacy of resuscitation with antioxidants in an animal model of hemorrhagic shock. Male Sprague-Dawley rats were anesthetized, and 27 mL/kg of blood was withdrawn from the carotid artery over 2 minutes. The animals remained in hemorrhagic shock for 45 minutes, followed by 1 hour of resuscitation. Experimental groups were as follows: 1) 15,000 u/kg superoxide dismutase (SOD) in 54 mL/kg lactated Ringer (LR); 2) 175,000 u/kg catalase (CAT) in LR; 3) 15,000 u/kg SOD+175,000 u/kg CAT in LR; 4) allopurinol in LR; 5) deferoxamine bound to pentafraction (DFO), 27 mL/kg; 6) pentafraction alone; and 7) LR alone. Compared with resuscitation with LR alone, SOD and allopurinol improved survival over 72 hours, P < 0.05. Survival with SOD+CAT was not different from LR alone. Deferoxamine bound to pentafraction did not increase survival over that with pentafraction alone. CAT had increased mortality compared to LR, P < 0.01. The efficacy of both SOD and allopurinol in decreasing mortality suggests the importance of superoxide radicals after hemorrhagic shock and resuscitation. These and other antioxidants are potential therapeutic agents in the clinical setting of trauma and hemorrhagic shock.

Trauma causes early release of soluble receptors for tumor necrosis factor

The importance of tumor necrosis factor (TNF) in the pathophysiology of trauma and hemorrhagic shock is not known. In addition, TNF bioactivity may be modulated by soluble forms of the 55-kd and 75-kd membrane receptors (TNFR). This study was undertaken to determine circulating levels of TNF and TNFR after trauma. Nine severely injured male patients were studied. The mean age was 30 +/- 10 years (range, 15-45). The mean Injury Severity Score (ISS) was 31.3 +/- 17.6 (range, 10-59), and the mean Revised Trauma Score (RTS), 5.7 +/- 2.2 (range, 0.7-7.8). Serum was obtained immediately upon arrival at our trauma center, within 1 hour of injury. The TNF and TNFR levels in the serum were measured using ELISA techniques. After trauma, 55-kd and 75-kd TNFR levels were significantly elevated above those of controls (6.99 +/- 4.57 ng/mL and 5.42 +/- 1.88 ng/mL, respectively, p < 0.01); TNF levels were not increased. Patient serum containing TNFR inhibited in vitro TNF cytotoxicity and correlated with 55-kd TNFR levels (p < 0.05). We conclude that TNF is a strong releasing factor for TNFR; the presence of TNFR may be indirect evidence that TNF is present after trauma, despite low measured levels. Both TNF and TNFR may be more important in trauma and hemorrhagic shock than previously thought.