scholarly journals Synechococcus sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daixi Liu ◽  
Jiajie Zhang ◽  
Chuanjuan Lü ◽  
Yongzhen Xia ◽  
Huaiwei Liu ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Oxygenic Photosynthesis ◽  
Gene Encoding ◽  
Aerobic Conditions ◽  
Sulfide:Quinone Oxidoreductase ◽  
Synechococcus Sp ◽  
Key Genes ◽  
New Perspective ◽  
Excessive Nutrients ◽  
Better Than

ABSTRACT Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that Synechococcus sp. strain PCC7002 (PCC7002), harboring an sqr gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S0, present as persulfide and polysulfide in the cell. The Δsqr mutant contained less cellular S0 and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria. IMPORTANCE Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δsqr mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S0, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.

scholarly journals Development of a novel Live Attenuated Influenza A Virus vaccine encoding the IgA-inducing protein

2021 ◽  
Author(s):  
C. Joaquín Cáceres ◽  
Stivalis Cardenas-Garcia ◽  
Aarti Jain ◽  
L. Claire Gay ◽  
Silvia Carnaccini ◽  
...  
Keyword(s):  
Influenza A ◽  
Protein Microarray ◽  
Natural Infection ◽  
Vaccine Safety ◽  
Gene Encoding ◽  
Lethal Challenge ◽  
Homologous Virus ◽  
Genes Encoding ◽  
Live Attenuated Influenza Virus ◽  
Better Than

Live attenuated influenza virus (LAIV) vaccines elicit a combination of systemic and mucosal immunity by mimicking a natural infection. To further enhance protective mucosal responses, we incorporated the gene encoding the IgA-inducing protein (IGIP) into the LAIV genomes of the cold-adapted A/Leningrad/134/17/57 (H2N2) strain (caLen) and the experimental attenuated backbone A/turkey/Ohio/313053/04 (H3N2) (OH/04att). Incorporation of IGIP into the caLen background led to a virus that grew poorly in prototypical substrates. In contrast, IGIP in the OH/04att background (IGIP-H1att) virus grew to titers comparable to the isogenic backbone H1att (H1N1) without IGIP. IGIP-H1att- and H1caLen-vaccinated mice were protected against lethal challenge with a homologous virus. The IGIP-H1att vaccine generated robust serum HAI responses in naïve mice against the homologous virus, equal or better than those obtained with the H1caLen vaccine. Analyses of IgG and IgA responses using a protein microarray revealed qualitative differences in humoral and mucosal responses between vaccine groups. Overall, serum and bronchoalveolar lavage samples from the IGIP-H1att group showed trends towards increased stimulation of IgG and IgA responses compared to H1caLen samples. In summary, introduction of genes encoding immunomodulatory functions into a candidate LAIV that can serve as natural adjuvants to improve overall vaccine safety and efficacy.

Genomic DNA methylation analysis revealed that BLNK is a key potential gene in the regulation of autophagy-related thyroid cancer progression

Genome ◽  
2021 ◽  
Author(s):  
Shengchi Zhang ◽  
Yongzhe Zheng ◽  
Guimin Zhang ◽  
Peng Lin ◽  
Wei Wang
Keyword(s):  
Dna Methylation ◽  
Thyroid Cancer ◽  
Cancer Progression ◽  
Protein Interactions ◽  
Methylation Status ◽  
Expression Change ◽  
Prognostic Analysis ◽  
Key Genes ◽  
New Perspective ◽  
The Relationship

The purpose of this study was to explore the relationship between autophagy and DNA methylation, and to identify key genes for autophagy-regulated thyroid cancer progression. We divided patients with thyroid cancer into high-autophagy score (AS) group and low-AS group based on their AS values. The results found that AS was associated with the distant metastasis of thyroid cancer, and adversely affected prognosis. Then, we screened 359 differently expressed genes (DEGs) with DNA methylation status consistent with gene expression change. Functional classification analysis demonstrated that the 359 DEGs consistent with DNA methylation status were significantly involved in adhesion, migration and differentiation of immune cells. To further screen the key genes in the autophagy-related thyroid cancer progression, we constructed a protein-protein interactions (PPI) network and performed prognostic analysis. B cell linker (BLNK) was identified as the key potential gene affecting autophagy-related thyroid cancer progression. Finally, we verified that BLNK promoted the proliferation of thyroid cancer cells, and BLNK expression was regulated by DNA methylation. Our research provides a new perspective for exploring the relationship between autophagy and DNA methylation during the progression of thyroid cancer, and provides a new target for the treatment of metastatic thyroid cancer.

scholarly journals Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

2019 ◽  
Vol 7 (10) ◽  
pp. 412 ◽  
Author(s):  
Pingping Cai ◽  
Zhuo Ning ◽  
Ningning Zhang ◽  
Min Zhang ◽  
Caijuan Guo ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Contaminated Aquifer ◽  
Genes Encoding ◽  
New Finding ◽  
Key Genes ◽  
Contaminated Aquifers ◽  
Metagenomics Analysis

In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.

scholarly journals Urine α-fetoprotein and orosomucoid 1 as biomarkers of hepatitis B virus-associated hepatocellular carcinoma

2020 ◽  
Vol 318 (2) ◽  
pp. G305-G312 ◽  
Author(s):  
Zhu Zhan ◽  
Yalan Guan ◽  
Kenley Mew ◽  
Weiqiong Zeng ◽  
Mingli Peng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Area Under The Curve ◽  
Screening Methods ◽  
Diagnostic Analysis ◽  
B Virus ◽  
New Perspective ◽  
Urine Reagent Strips ◽  
Better Than

Hepatocellular carcinoma (HCC) is the sixth common malignant tumor worldwide, but current efficient and convenient screening methods remain lacking. This study aimed to discover a diagnostic or a screening biomarker from the urine of hepatitis B virus (HBV)-related HCC patients. We used iTRAQ coupled with mass spectrometry to identify candidate urinary proteins in a discovery cohort ( n = 40). The selected proteins were confirmed using ELISA in a validation cohort ( n = 140). Diagnostic performance of the selected proteins was assessed using receiver operating characteristic (ROC) and qualitative diagnostic analysis. A total of 96 differentially expressed proteins were identified. Urinary α-fetoprotein (u-AFP) and orosomucoid 1 (u-ORM1) were selected as target proteins by bioinformatics analysis and were significantly higher in HCC than in non-HCC patients, as validated by Western blot analysis and ELISA. u-AFP had a strong correlation with serum AFP-L3 (Pearson’s r = 0.944, P < 0.0001), indicating that u-AFP may be derived from circulating blood. The area under the curve (AUC) of u-AFP was 0.795 with a sensitivity of 62.5% and a specificity of 95.4%, which showed no significantly difference with serum AFP (se-AFP). The AUC was 0.864 as u-AFP and u-ORM1 were combined, and they performed much better than u-AFP or u-ORM1 alone. Qualitative diagnostic analysis showed that the positive predictive value of u-AFP was 90.1% and the diagnostic sensitivity of parallel combination of u-AFP and u-ORM1 was 85.1%. Taken together, AFP and ORM1 in the urine may be used as a diagnostic or screening biomarker of HCC, and studies on large samples are needed to validate the result. NEW & NOTEWORTHY This study provides a novel way to find biomarkers of hepatocellular carcinoma (HCC) and a new perspective of α-fetoprotein clinical application. The urine reagent strips may be helpful in high epidemic areas of HCC and in low-resource settings.

scholarly journals Cryptic oxygen cycling in anoxic marine zones

2017 ◽  
Vol 114 (31) ◽  
pp. 8319-8324 ◽  
Author(s):  
Emilio Garcia-Robledo ◽  
Cory C. Padilla ◽  
Montserrat Aldunate ◽  
Frank J. Stewart ◽  
Osvaldo Ulloa ◽  
...  
Keyword(s):  
Surface Layer ◽  
Carbon Fixation ◽  
Nitrogen Loss ◽  
Biogeochemical Cycling ◽  
Oxygenic Photosynthesis ◽  
Nitrite Oxidation ◽  
Tight Coupling ◽  
Expression Of Genes ◽  
Aerobic Processes ◽  
Oxygen Cycling

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteriaProchlorococcusspp. Free O2levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

scholarly journals Potassium Transporter LrKUP8 Is Essential for K+ Preservation in Lycium ruthenicum, A Salt-Resistant Desert Shrub

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 600
Author(s):  
Fengbin Dai ◽  
Aijia Li ◽  
Shupei Rao ◽  
Jinhuan Chen
Keyword(s):  
Salt Stress ◽  
Salt Adaptation ◽  
Ion Content ◽  
K Uptake ◽  
Gene Encoding ◽  
Major Constraint ◽  
Lycium Ruthenicum ◽  
Balance Mechanism ◽  
Tolerance To Salinity ◽  
Better Than

Salt stress is a major constraint for many crops and trees. A wild species of Goji named Lycium ruthenicum is an important economic halophyte in China and has an extremely high tolerance to salinity. L. ruthenicum grows in saline soil and is known as a potash-rich species. However, its salt adaptation strategies and ion balance mechanism remains poorly understood. Potassium (K+) is one of the essential macronutrients for plant growth and development. In this study, a putative salt stress-responsive gene encoding a HAK (high-affinity K+)/KUP (K+ uptake)/KT (K+ transporter) transporter was cloned and designated as LrKUP8. This gene belongs to the cluster II group of the KT/HAK/KUP family. The expression of LrKUP8 was strongly induced under high NaCl concentrations. The OE-LrKUP8 calli grew significantly better than the vector control calli under salt stress conditions. Further estimation by ion content and micro-electrode ion flux indicated a relative weaker K+ efflux in the OE-LrKUP8 calli than in the control. Thus, a key gene involved in K+ uptake under salt condition was functionally characterized using a newly established L. ruthenicum callus transformation system. The importance of K+ regulation in L. ruthenicum under salt tolerance was highlighted.

scholarly journals AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Abhijeet Singh ◽  
Bettina Müller ◽  
Hans-Henrik Fuxelius ◽  
Anna Schnürer
Keyword(s):  
Carbon Fixation ◽  
Sequence Data ◽  
Gene Encoding ◽  
Formyltetrahydrofolate Synthetase ◽  
Protein Levels ◽  
Acetogenic Bacteria ◽  
Blast Database ◽  
Key Enzyme ◽  
Chemolithoautotrophic Bacteria ◽  
Taxonomic Studies

Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

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