scholarly journals Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

2019 ◽  
Author(s):  
Kshitij Tandon ◽  
Pei-Wen Chiang ◽  
Chih-Ying Lu ◽  
Naohisa Wada ◽  
Shan-Hua Yang ◽  
...  
Keyword(s):  
Sole Carbon Source ◽  
Genomic Analysis ◽  
Sulfur Cycle ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Coa Transferase ◽  
Complete Genomes ◽  
Central Carbon

AbstractDominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase—a dddD gene homolog found in all E. acroporae strains—and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

scholarly journals Unexpected and widespread connections between bacterial glycogen and trehalose metabolism

Microbiology ◽  
2011 ◽  
Vol 157 (6) ◽  
pp. 1565-1572 ◽  
Author(s):  
Govind Chandra ◽  
Keith F. Chater ◽  
Stephen Bornemann
Keyword(s):  
Drug Target ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Classical Pathway ◽  
Outer Capsule ◽  
Trehalose Metabolism ◽  
Glucan Synthesis

Glycogen, a large α-glucan, is a ubiquitous energy storage molecule among bacteria, and its biosynthesis by the classical GlgC-GlgA pathway and its degradation have long been well understood – or so we thought. A second pathway of α-glucan synthesis, the four-step GlgE pathway, was recently discovered in mycobacteria. It requires trehalose as a precursor, and has been genetically validated as a novel anti-tuberculosis drug target. The ability to convert glycogen into trehalose was already known, so the GlgE pathway provides a complementary way of cycling these two metabolites. As well as containing cytosolic storage glycogen, mycobacteria possess an outer capsule containing a glycogen-like α-glucan that is implicated in immune system evasion, so the GlgE pathway might be linked to capsular α-glucan biosynthesis. Another pathway (the Rv3032 pathway) for α-glucan biosynthesis in mycobacteria generates a methylglucose lipopolysaccharide thought to be associated with fatty acid metabolism. A comparative genomic analysis was carried out to evaluate the occurrence and role of the classical pathway, the new GlgE pathway and the Rv3032 pathway across bacteria occupying very different ecological niches. The GlgE pathway is represented in 14 % of sequenced genomes from diverse bacteria (about half as common as the classical pathway), while the Rv3032 pathway is restricted with few exceptions to mycobacteria, and the GlgB branching enzyme, usually presumed to be associated with the classical pathway, correlates more strongly with the new GlgE pathway. The microbiological implications of recent discoveries in the light of the comparative genomic analysis are discussed.

scholarly journals Comparative Genomic Analysis Reveals a Critical Role of De Novo Nucleotide Biosynthesis for Saccharomyces cerevisiae Virulence

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0122382 ◽  
Author(s):  
Roberto Pérez-Torrado ◽  
Silvia Llopis ◽  
Benedetta Perrone ◽  
Rocío Gómez-Pastor ◽  
Bernhard Hube ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Critical Role ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Nucleotide Biosynthesis

scholarly journals NCoR1 and SMRT fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling

2021 ◽  
Author(s):  
A. Jha ◽  
A. Ahad ◽  
G. P. Mishra ◽  
K. Sen ◽  
S. Smita ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Tumor Burden ◽  
Differential Regulation ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Cell Frequency ◽  
Stat3 Signaling ◽  
Immune Pathology ◽  
Fine Tune

AbstractDendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4+and CD8+T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion repressed mTOR-STAT3-IL10 signaling in cDC1 by down-regulating NR4A1. Besides, NFkBIA and SOCS3 were down-regulated in SMRT knockdown cDC1, supporting increased production of inflammatory cytokines. Moreover, adoptive transfer of SMRT knockdown cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8+T-cell frequency, respectively. We also depicted decreasedSmrtexpression in Rheumatoid Arthritis, a Th1/Th17 disease.

scholarly journals Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible

2021 ◽  
pp. 100015
Author(s):  
Eamon O. Murchu ◽  
Sinead O'Neill ◽  
Paula Byrne ◽  
Cillian De Gascun ◽  
Michelle O'Neill ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis

3 Biotech ◽  
2021 ◽  
Vol 11 (6) ◽  
Author(s):  
Kai Huang ◽  
Bo Zhang ◽  
Yu Chen ◽  
Zhe-Ming Wu ◽  
Zhi-Qiang Liu ◽  
...  
Keyword(s):  
Amphotericin B ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic
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