scholarly journals Biotechnological Production of Cyclic Dinucleotides – Challenges and Opportunities

2021 ◽  
Author(s):  
Tabea Bartsch ◽  
Martin Becker ◽  
Jascha Rolf ◽  
Katrin Rosenthal ◽  
Stephan Lütz
Keyword(s):  
Biotechnological Production ◽  
Challenges And Opportunities ◽  
Cyclic Dinucleotides

scholarly journals Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

2019 ◽  
Vol 15 ◽  
pp. 2889-2906 ◽  
Author(s):  
Eric J N Helfrich ◽  
Geng-Min Lin ◽  
Christopher A Voigt ◽  
Jon Clardy
Keyword(s):  
Biosynthetic Pathway ◽  
Pathway Engineering ◽  
Biosynthetic Pathways ◽  
Assembly Lines ◽  
Terpene Biosynthesis ◽  
Biotechnological Production ◽  
Genetic Potential ◽  
Challenges And Opportunities ◽  
Tailoring Enzymes ◽  
Single Enzyme

Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.

Continuous hydrogenolysis of acetal-stabilized lignin in flow

2021 ◽  
Author(s):  
Wu Lan ◽  
Yuan Peng Du ◽  
Songlan Sun ◽  
Jean Behaghel de Bueren ◽  
Florent Héroguel ◽  
...  
Keyword(s):  
Steady State ◽  
Challenges And Opportunities

We performed a steady state high-yielding depolymerization of soluble acetal-stabilized lignin in flow, which offered a window into challenges and opportunities that will be faced when continuously processing this feedstock.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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