Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas-fermenting Clostridium ljungdahlii.

Gas-fermenting Clostridium species can convert one-carbon gases (CO2 /CO) into a variety of chemicals and fuels, showing excellent application prospects in green biological manufacturing. The discovery of crucial genes and proteins with novel functions is important for understanding and further optimization of these autotrophic bacteria. Here, we report that the Clostridium ljungdahlii BirA protein (ClBirA) plays a pleiotropic regulator role, which, together with its biotin protein ligase (BPL) activity, enables an effective control of autotrophic growth of C. ljungdahlii. The structural modulation of ClBirA, combined with the in vivo and in vitro analyses, further reveals the action mechanism of ClBirA's dual roles as well as their interaction in C. ljungdahlii. Importantly, an atypical, flexible architecture of the binding site was found to be employed by ClBirA in the regulation of a lot of essential pathway genes, thereby expanding BirA's target genes to a broader range in clostridia. Based on these findings, molecular modification of ClBirA was performed, and an improved cellular performance of C. ljungdahlii was achieved in gas fermentation. This work reveals a previously unknown potent role of BirA in gas-fermenting clostridia, providing new perspective for understanding and engineering these autotrophic bacteria.

The Small RNA sr8384 Is a Crucial Regulator of Cell Growth in Solventogenic Clostridia.

Small RNAs (sRNAs) are crucial regulatory molecules in organisms and are well-known not only for their roles in the control of diverse crucial biological processes but also for their value in regulation rewiring. However, to date, in Gram-positive anaerobic solventogenic clostridia (a group of important industrial bacteria with exceptional substrate and product diversity), sRNAs remain minimally explored, and thus there is a lack of detailed understanding regarding these important molecules and their use as targets for genetic improvement. Here, we performed large-scale phenotypic screens of a transposon-mediated mutant library of Clostridium acetobutylicum, a typical solventogenic clostridial species, and discovered a novel sRNA (sr8384) that functions as a crucial regulator of cell growth. Comparative transcriptomic data combined with genetic and biochemical analyses revealed that sr8384 acts as a pleiotropic regulator and controls multiple targets that are associated with crucial biological processes through direct or indirect interactions. Notably, the in vivo expression level of sr8384 determined the cell growth rate, thereby affecting the solvent titer and productivity. These findings indicate the importance of the sr8384-mediated regulatory network in C. acetobutylicum Furthermore, a homolog of sr8384 was discovered and proven to be functional in another important Clostridium species, C. beijerinckii, suggesting the potential broad role of this sRNA in clostridia. Our work showcases a previously unknown potent and complex role of sRNAs in clostridia, providing new opportunities for understanding and engineering these anaerobes.IMPORTANCE The uses of sRNAs as new resources for functional studies and strain modifications are promising strategies in microorganisms. However, these crucial regulatory molecules have hardly been explored in industrially important solventogenic clostridia. Here, we identified sr8384 as a novel determinant sRNA controlling the cell growth of solventogenic Clostridium acetobutylicum Based on a detailed functional analysis, we further reveal the pleiotropic function of sr8384 and its multiple direct and indirect crucial targets, which represents a valuable source for understanding and optimizing this anaerobe. Of note, manipulation of this sRNA achieves improved cell growth and solvent synthesis. Our findings provide a new perspective for future studies on regulatory sRNAs in clostridia.

Roles of two-component system AfsQ1/Q2 in regulating biosynthesis of the yellow-pigmented coelimycin P2 in Streptomyces coelicolor.

We previously demonstrated that in Streptomyces coelicolor two-component system AfsQ1/Q2 activates the production of the yellow-colored coelimycin P2 (also named as yCPK) on glutamate-supplemented minimal medium, and the response regulator AfsQ1 could specifically bind to the intergenic region between two structural genes, cpkA and cpkD Here, a more in-depth investigation was performed to elucidate the mechanism underlying the role of AfsQ1/Q2 in regulating coelimycin P2 biosynthesis. Deletion of afsQ1/Q2 resulted in markedly decreased expression of the whole coelimycin P2 biosynthetic gene cluster. Electrophoretic mobility shift assays revealed that AfsQ1 bound only to the target site identified previously, but not to any other promoters in the gene cluster. Mutations of AfsQ1-binding motif only resulted in drastically reduced transcription of the cpkA/B/C operon (encoding three type I polyketide synthases) and intriguingly, led to enhanced expression of some coelimcyin P2 genes, particularly accA1 and scF These results suggested the direct role of AfsQ1/Q2 in regulating coelimycin production, which is directly mediated by the structural genes, but not the cluster-situated regulatory genes, and also implied that other unknown mechanisms may be involved in AfsQ1/Q2-mediated regulation of coelimycin P2 biosynthesis.

Ammonium acetate enhances solvent production by Clostridium acetobutylicum EA 2018 using cassava as a fermentation medium.

Cassava, due to its high starch content and low cost, is a promising candidate substrate for large-scale fermentation processes aimed at producing the solvents acetone, butanol and ethanol (ABE). However, the solvent yield from the fermentation of cassava reaches only 60% of that achieved by fermenting corn. We have found that the addition of ammonium acetate (CH(3)COONH(4)) to the cassava medium significantly promotes solvent production from cassava fermented by Clostridium acetobutylicum EA 2018, a mutant with a high butanol ratio. When cassava medium was supplemented with 30 mM ammonium acetate, the acetone, butanol and total solvent production reached 5.0, 13.0 and 19.4 g/l, respectively, after 48 h of fermentation. This level of solvent production is comparable to that obtained from corn medium. Both ammonium (NH(4) (+)) and acetate (CH(3)COO(-)) were required for increased solvent synthesis. We also demonstrated substantially increased acetic and butyric acid accumulation during the acidogenesis phase as well as greater acid re-assimilation during the solventogenesis period in ammonium acetate-supplemented cassava medium. Reverse transcription-polymerase chain reaction analysis indicated that the transcription of several genes encoding enzymes related to acidogenesis and solventogenesis in C. acetobutylicum EA 2018 were enhanced by the addition of ammonium acetate to the cassava medium.

Nonlinear current response of micro electroporation and resealing dynamics for human cancer cells.

This paper presents a novel method to measure the dynamic process of membrane permeability during electroporation (EP) on microchips for human cancer cells. Micro EP chips with three-dimensional gold electrodes accommodating a single cell in between were fabricated with a modified electroplating process. Electrochemical impedance spectroscopy (EIS) was carried out with an electrochemistry analyzer on micro EP chips and a nonlinear equivalent circuit model was proposed to describe the dynamic response of the whole system. Using such a method, micro EP current was isolated from undesired leakage current to study the corresponding electroporation dynamics under different input voltages. In addition, cell membrane recovery dynamics after electroporation was also studied and the resealing time constants were determined for different pulse treatments.

Using a micro electroporation chip to determine the optimal physical parameters in the uptake of biomolecules in HeLa cells.

In this study, a new micro electroporation (EP) cell chip with three-dimensional (3D) electrodes was fabricated by means of MEMS technology, and tested on cervical cancer (HeLa) cells. Extensive statistical data of the threshold electric field and pulse duration were determined to construct an EP "phase diagram", which delineates the boundaries for 1) effective EP of five different size molecules and 2) electric cell lysis at the single-cell level. In addition, these boundary curves (i.e., electric field versus pulse duration) were fitted successfully with an exponential function with three constants. We found that, when the molecular size increases, the corresponding electroporation boundary becomes closer to the electric cell lysis boundary. Based on more than 2000 single-cell measurements on five different size molecules, the critical size of molecule was found to be approximately 40 kDa. Comparing to the traditional instrument, MEMS-based micro electroporation chip can greatly shorten the experimental time.

Micro pulsed radio-frequency electroporation chips.

Electroporation (EP) is one of the most important physical methods in biotechnology, which employs electrical pulses to transiently permeabilize cell membranes. In this study, a new micro pulsed radio-frequency electroporation cell (microPREP) chip was fabricated using a lift-off technique and SU-8 photolithography. The biological tests were carried out using three different plant protoplasts (cabbage, spinach and oil rape) on the micro EP chip and a pulsed RF electric field was applied to the microchip. The variations of fluorescent intensity and cell viability as functions of the electric pulse amplitude and duration time during the electroporation process were studied in detail at the single-cell level. Using such chip design and test method, one can easily optimize the efficiency and cell viability. Also, a large amount of statistical data can be quickly obtained. Finally, results of this parametric study were presented in the "phase diagram", from which the critical electric field for inducing single-cell electroporation under different conditions can be clearly determined.