scholarly journals Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kristopher Kieft ◽  
Zhichao Zhou ◽  
Rika E. Anderson ◽  
Alison Buchan ◽  
Barbara J. Campbell ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Niche Differentiation ◽  
Host Cells ◽  
Freshwater Lakes ◽  
Inorganic Sulfur ◽  
Metabolic Genes ◽  
Fitness Benefits ◽  
Auxiliary Metabolic Genes ◽  
Hydrothermal Environments

AbstractMicrobial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

scholarly journals Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

2020 ◽  
Author(s):  
Kristopher Kieft ◽  
Zhichao Zhou ◽  
Rika Anderson ◽  
Alison Buchan ◽  
Barbara Campbell ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Niche Differentiation ◽  
Host Cells ◽  
Freshwater Lakes ◽  
Inorganic Sulfur ◽  
Metabolic Genes ◽  
Fitness Benefits ◽  
Auxiliary Metabolic Genes ◽  
Hydrothermal Environments

Abstract Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

scholarly journals Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

2020 ◽  
Author(s):  
Kristopher Kieft ◽  
Zhichao Zhou ◽  
Rika E. Anderson ◽  
Alison Buchan ◽  
Barbara J. Campbell ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Niche Differentiation ◽  
Host Cells ◽  
Freshwater Lakes ◽  
Inorganic Sulfur ◽  
Metabolic Genes ◽  
Fitness Benefits ◽  
Auxiliary Metabolic Genes ◽  
Hydrothermal Environments

ABSTRACTMicrobial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

scholarly journals Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

2021 ◽  
Author(s):  
Mihnea R. Mangalea ◽  
David Paez-Espino ◽  
Kristopher Kieft ◽  
Anushila Chatterjee ◽  
Jennifer A. Seifert ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
At Risk ◽  
Autoimmune Disease ◽  
Intestinal Microbiota ◽  
Disease Development ◽  
Metabolic Potential ◽  
Metabolic Genes ◽  
Auxiliary Metabolic Genes ◽  
Citrullinated Protein ◽  
Insight Into

SUMMARYRheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Lachnospiraceae phages, and originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes (AMGs) which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.

scholarly journals Construction and Validation of a Metabolic Reprogramming Related Prognostic Model for Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Xiaohong - Liu ◽  
Qian - Xu ◽  
Zi-Jing - Li ◽  
Bin - Xiong
Keyword(s):  
Hepatocellular Carcinoma ◽  
Regression Analysis ◽  
Risk Score ◽  
Prognostic Model ◽  
Cox Regression ◽  
Expression Profiles ◽  
Prognostic Significance ◽  
Metabolic Reprogramming ◽  
Cox Regression Analysis ◽  
Metabolic Genes

Abstract BackgroundMetabolic reprogramming is an important hallmark in the development of malignancies. Numerous metabolic genes have been demonstrated to participate in the progression of hepatocellular carcinoma (HCC). However, the prognostic significance of the metabolic genes in HCC remains elusive. MethodsWe downloaded the gene expression profiles and clinical information from the GEO, TCGA and ICGC databases. The differently expressed metabolic genes were identified by using Limma R package. Univariate Cox regression analysis and LASSO (Least absolute shrinkage and selection operator) Cox regression analysis were utilized to uncover the prognostic significance of metabolic genes. A metabolism-related prognostic model was constructed in TCGA cohort and validated in ICGC cohort. Furthermore, we constructed a nomogram to improve the accuracy of the prognostic model by using the multivariate Cox regression analysis.ResultsThe high-risk score predicted poor prognosis for HCC patients in the TCGA cohort, as confirmed in the ICGC cohort (P < 0.001). And in the multivariate Cox regression analysis, we observed that risk score could act as an independent prognostic factor for the TCGA cohort (HR (hazard ratio) 3.635, 95% CI (confidence interval)2.382-5.549) and the ICGC cohort (HR1.905, 95%CI 1.328-2.731). In addition, we constructed a nomogram for clinical use, which suggested a better prognostic model than risk score.ConclusionsOur study identified several metabolic genes with important prognostic value for HCC. These metabolic genes can influence the progression of HCC by regulating tumor biology and can also provide metabolic targets for the precise treatment of HCC.

scholarly journals Identification of differentially expressed circular RNAs in HeLa cells infected with Chlamydia trachomatis

2019 ◽  
Vol 77 (7) ◽  
Author(s):  
Yuanjun Liu ◽  
Chunmin Hu ◽  
Yina Sun ◽  
Haoqing Wu ◽  
Xiaojun Chen ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Signaling Pathways ◽  
Hela Cells ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Host Cells ◽  
Differentially Expressed ◽  
Chlamydia Infection ◽  
Circular Rnas ◽  
Mrna Microarray

ABSTRACT Non-coding circular RNAs (circRNAs) have been shown to have important roles in many diseases; however, no study has indicated circRNAs are involved in Chlamydia trachomatis infection. In this study, we used circRNA microarray to measure the global circRNA expression profiles in HeLa cells with or without C. trachomatis serovar E (Ct.E) infection. CircRNA/miRNA/mRNA interactions were predicted and bioinformatics analyses were performed. The differentially expressed circRNAs were selected according to our criterion for validation by reverse-transcription and quantitative polymerase chain reaction (RT-qPCR). The mRNA microarray was used to detect the mRNA expression profiles after Ct.E infection. Among 853 differentially expressed circRNAs, 453 were upregulated and 400 were downregulated after Ct.E infection. Target miRNAs and miRNA-targeted mRNAs of these circRNAs were predicted. RT-qPCR analysis indicated hsa_circRNA_001226, hsa_circRNA_007046 and hsa_circRNA_400027 were elevated similar to those determined in the circRNA microarray analysis. The mRNA microarray results showed 915 genes were upregulated and 619 genes were downregulated after Ct.E infection. Thirty-four differentially expressed genes overlapped in the bioinformatics and mRNA microarray results. KEGG pathway analysis revealed several signaling pathways, including endocytosis, MAPK and PI3P-Akt signaling pathways, that were targeted by circRNAs may play important roles in Chlamydia infection. This study provides evidence that circRNAs in host cells are involved in the process of Chlamydia infection.

scholarly journals The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

Virology ◽  
2016 ◽  
Vol 499 ◽  
pp. 219-229 ◽  
Author(s):  
Lisa T. Crummett ◽  
Richard J. Puxty ◽  
Claudia Weihe ◽  
Marcia F. Marston ◽  
Jennifer B.H. Martiny
Keyword(s):  
Metabolic Genes ◽  
Auxiliary Metabolic Genes

scholarly journals CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants

2015 ◽  
Vol 197 (19) ◽  
pp. 3191-3205 ◽  
Author(s):  
Yun-Juan Bao ◽  
Zhong Liang ◽  
Jeffrey A. Mayfield ◽  
Shaun W. Lee ◽  
Victoria A. Ploplis ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Broad Spectrum ◽  
Virulence Genes ◽  
Expression Profiles ◽  
Altered Expression ◽  
Content Type ◽  
Metabolic Genes ◽  
A Genome ◽  
Group A ◽  
Regulated Gene Expression

ABSTRACTThe two-componentcontrolofvirulence (Cov) regulator (R)-sensor (S) (CovRS) regulates the virulence ofStreptococcus pyogenes(group AStreptococcus[GAS]). Inactivation of CovS during infection switches the pathogenicity of GAS to a more invasive form by regulating transcription of diverse virulence genes via CovR. However, the manner in which CovRS controls virulence through expression of extended gene families has not been fully determined. In the current study, the CovS-regulated gene expression profiles of a hypervirulentemm23GAS strain (M23ND/CovS negative [M23ND/CovS−]) and a noninvasive isogenic strain (M23ND/CovS+), under different growth conditions, were investigated. RNA sequencing identified altered expression of ∼349 genes (18% of the chromosome). The data demonstrated that M23ND/CovS−achieved hypervirulence by allowing enhanced expression of genes responsible for antiphagocytosis (e.g.,hasABC), by abrogating expression of toxin genes (e.g.,speB), and by compromising gene products with dispensable functions (e.g.,sfb1). Among these genes, several (e.g.,parEandparC) were not previously reported to be regulated by CovRS. Furthermore, the study revealed that CovS also modulated the expression of a broad spectrum of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination, where the bacteria encounter large variations in available nutrients, thus restructuring metabolism of GAS for adaption to diverse growth environments. From constructing a genome-scale metabolic model, we identified 16 nonredundant metabolic gene modules that constitute unique nutrient sources. These genes were proposed to be essential for pathogen growth and are likely associated with GAS virulence. The genome-wide prediction of genes associated with virulence identifies new candidate genes that potentially contribute to GAS virulence.IMPORTANCEThe CovRS system modulates transcription of ∼18% of the genes in theStreptococcus pyogenesgenome. Mutations that inactivate CovR or CovS enhance the virulence of this bacterium. We determined complete transcriptomes of a naturally CovS-inactivated invasive deep tissue isolate of anemm23strain ofS. pyogenes(M23ND) and its complemented avirulent variant (CovS+). We identified diverse virulence genes whose altered expression revealed a genetic switching of a nonvirulent form of M23ND to a highly virulent strain. Furthermore, we also systematically uncovered for the first time the comparative levels of expression of a broad spectrum of metabolic genes, which reflected different metabolic needs of the bacterium as it invaded deeper tissue of the human host.

scholarly journals A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1081 ◽  
Author(s):  
Zengmeng Wang ◽  
Jiulong Zhao ◽  
Long Wang ◽  
Chengcheng Li ◽  
Jianhui Liu ◽  
...  
Keyword(s):  
Burst Size ◽  
Coastal Sediments ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Lytic Phage ◽  
Host Interactions ◽  
Metabolic Genes ◽  
Double Stranded Dna ◽  
Auxiliary Metabolic Genes ◽  
Structure Assembly

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.

scholarly journals Encephalitozoon cuniculi and Vittaforma corneae (Phylum Microsporidia) inhibit staurosporine-induced apoptosis in human THP-1 macrophages in vitro

Parasitology ◽  
2018 ◽  
Vol 146 (5) ◽  
pp. 569-579 ◽  
Author(s):  
Yuliya Y. Sokolova ◽  
Lisa C. Bowers ◽  
Xavier Alvarez ◽  
Elizabeth S. Didier
Keyword(s):  
Expression Profiles ◽  
Life Cycles ◽  
Host Cells ◽  
Human Macrophage ◽  
Inflammasome Activation ◽  
Encephalitozoon Cuniculi ◽  
Apoptosis Pathway ◽  
Intrinsic Apoptosis Pathway ◽  
Induced Apoptosis

AbstractObligately intracellular microsporidia regulate their host cell life cycles, including apoptosis, but this has not been evaluated in phagocytic host cells such as macrophages that can facilitate infection but also can be activated to kill microsporidia. We examined two biologically dissimilar human-infecting microsporidia species, Encephalitozoon cuniculi and Vittaforma corneae, for their effects on staurosporine-induced apoptosis in the human macrophage-differentiated cell line, THP1. Apoptosis was measured after exposure of THP-1 cells to live and dead mature organisms via direct fluorometric measurement of Caspase 3, colorimetric and fluorometric TUNEL assays, and mRNA gene expression profiles using Apoptosis RT2 Profiler PCR Array. Both species of microsporidia modulated the intrinsic apoptosis pathway. In particular, live E. cuniculi spores inhibited staurosporine-induced apoptosis as well as suppressed pro-apoptosis genes and upregulated anti-apoptosis genes more broadly than V. corneae. Exposure to dead spores induced an opposite effect. Vittaforma corneae, however, also induced inflammasome activation via Caspases 1 and 4. Of the 84 apoptosis-related genes assayed, 42 (i.e. 23 pro-apoptosis, nine anti-apoptosis, and 10 regulatory) genes were more affected including those encoding members of the Bcl2 family, caspases and their regulators, and members of the tumour necrosis factor (TNF)/TNF receptor R superfamily.

scholarly journals Global Regulation of the Response to Sulfur Availability in the Cheese-Related BacteriumBrevibacterium aurantiacum

2010 ◽  
Vol 77 (4) ◽  
pp. 1449-1459 ◽  
Author(s):  
Marie-Pierre Forquin ◽  
Agnès Hébert ◽  
Aurélie Roux ◽  
Julie Aubert ◽  
Caroline Proux ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Metabolic Reconstruction ◽  
Sulfate Assimilation ◽  
Sulfur Starvation ◽  
Expression Of Genes ◽  
Transsulfuration Pathway ◽  
Sulfate Assimilation Pathway ◽  
Genes Encoding ◽  
Sulfur Containing

ABSTRACTIn this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability inBrevibacterium aurantiacum. In agreement with the growth ofB. aurantiacumin the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysEandcysK) or homocysteine (metXandmetY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles ofB. aurantiacumATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression ofmetX,metY,metE1,metE2, andBL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.

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