Cold shock proteins improve E. coli cell‐free synthesis in terms of soluble yields of aggregation‐prone proteins

An internal loop region is responsible for inherent target specificity of bacterial cold-shock proteins

Cold-shock proteins (Csps), of around 70 amino acids, share a protein fold for the cold-shock domain (CSD) that contains RNA-binding motifs, RNP1 and RNP2, and constitute one family of bacterial RNA-binding proteins. Despite similar amino acid composition, Csps have been shown to individually possess inherent specific functions. Here, we identify the molecular differences in Csps that allow selective recognition of RNA targets. Using chimeras and mutants of Escherichia coli CspD and CspA, we demonstrate that Lys43-Ala44 in an internal loop of CspD, and the N-terminal portion with Lys4 of CspA, are important for determining their target specificities. Pull-down assays suggest that these distinct specificities reflect differences in the ability to act on the target RNAs rather than differences in binding to the RNA targets. A phylogenetic tree constructed from 1,573 Csps reveals that the Csps containing Lys-Ala in the loop form a monophyletic clade, and the members in this clade are shown to have target specificities similar to E. coli CspD. The phylogenetic tree also finds a small cluster of Csps containing Lys-Glu in the loop, and these exhibit a different specificity than E. coli CspD. Examination of this difference suggests a role of the loop of CspD-type proteins in recognition of specific targets. Additionally, each identified type of Csp shows a different distribution pattern among bacteria. Our findings provide a basis for subclassification of Csps based on target RNA specificity, which will be useful for understanding the functional specialization of Csps.

Development of the Low-Temperature Inducible System for Recombinant Protein Production in Escherichia coli Nissle 1917

The pET system is commonly used for producing foreign proteins in Escherichia coli, but its reliance on the costly and metabolically demanding inducer IPTG limits its industrial use. This study engineered a low-temperature inducible system (LTIS) in E. coli Nissle 1917 (EcN) by combining the T7 expression system with the thermal inducible mechanism CI857-λPRPL to generate the new LTIS strain, ENL7P. The strain ENL7P-sfGFP-Km underwent overnight culture at 37 °C for 14-16 h, followed by subculturing at 30 °C for 24 h. This resulted in a notable 5.53-fold increase in the sfGFP induction rate when the strain was cultivated under 37-30 °C conditions. Moreover, gene expression was induced using a two-stage strategy. Initially, the strain was cultured overnight at 39 °C for 14-16 h, followed by a subculture at 30 °C for 6 h, and finally, another subculture at 30 °C for 24 h. This cultivation strategy led to an impressive 158.37-fold induction rate for sfGFP. Similar effects could be achieved through utilization of the LTIS system for inducing the production of thermophilic trehalose synthase from Thermus antranikianii (TaTS). The results of this study proved that the LTIS system has the potential for industrial applications.

Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods

Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ⁷⁰ promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.

Synthesis of an Anti-CD7 Recombinant Immunotoxin Based on PE24 in CHO and E. coli Cell-Free Systems

Recombinant immunotoxins (RITs) are an effective class of agents for targeted therapy in cancer treatment. In this article, we demonstrate the straight-forward production and testing of an anti-CD7 RIT based on PE24 in a prokaryotic and a eukaryotic cell-free system. The prokaryotic cell-free system was derived from Escherichia coli BL21 StarTM (DE3) cells transformed with a plasmid encoding the chaperones groEL/groES. The eukaryotic cell-free system was prepared from Chinese hamster ovary (CHO) cells that leave intact endoplasmic reticulum-derived microsomes in the cell-free reaction mix from which the RIT was extracted. The investigated RIT was built by fusing an anti-CD7 single-chain variable fragment (scFv) with the toxin domain PE24, a shortened variant of Pseudomonas Exotoxin A. The RIT was produced in both cell-free systems and tested for antigen binding against CD7 and cell killing on CD7-positive Jurkat, HSB-2, and ALL-SIL cells. CD7-positive cells were effectively killed by the anti-CD7 scFv-PE24 RIT with an IC50 value of 15 pM to 40 pM for CHO and 42 pM to 156 pM for E. coli cell-free-produced RIT. CD7-negative Raji cells were unaffected by the RIT. Toxin and antibody domain alone did not show cytotoxic effects on either CD7-positive or CD7-negative cells. To our knowledge, this report describes the production of an active RIT in E. coli and CHO cell-free systems for the first time. We provide the proof-of-concept that cell-free protein synthesis allows for on-demand testing of antibody−toxin conjugate activity in a time-efficient workflow without cell lysis or purification required.

Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic Pressure

Microbes living in extreme environments often adopt strategies for survival, however, only a few studies have examined the adaptive mechanism of deep-sea bacteria in in-situ environments. In this study, transcriptomic data of the deep-sea piezotolerant and psychrotolerant actinomycete Microbacterium sediminis YLB-01 under the conditions of NPNT (normal temperature and pressure: 28 °C, 0.1 MPa), HPNT (normal temperature and high pressure: 28 °C, 30 MPa), NPLT (low temperature and atmospheric pressure: 4 °C, 0.1 MPa) and HPLT (low temperature and high pressure: 4 °C, 30 MPa) were examined and compared. Transcriptome results showed that M. sediminis YLB-01 responds to deep-sea low temperature under high-pressure environments by upregulating the ABC transport system, DNA damage repair response, pentose phosphate pathway, amino acid metabolism and fatty acid metabolism, while down-regulating division, oxidative phosphorylation, the TCA cycle, pyruvate metabolism, ion transport and peptidoglycan biosynthesis. Seven key genes specifically expressed under HPLT conditions were screened, and these genes are present in many strains that are tolerant to low temperatures and high pressures. This study provides transcription level insights into the tolerance mechanisms of M. sediminis YLB-01 in a simulated deep-sea in situ environment.

Plant-Based Cell-Free Transcription and Translation of Recombinant Proteins

Plant cell-free lysates contain all the cellular components of the protein biosynthesis machinery, providing an alternative to intact plant cells, tissues, and whole plants for the production of recombinant proteins. Cell-free lysates achieve rapid protein production (within hours or days) and allow the synthesis of proteins that are cytotoxic or unstable in living cells. The open nature of cell-free lysates and their homogeneous and reproducible performance is ideal for protein production, especially for screening applications, allowing the direct addition of nucleic acid templates encoding proteins of interest, as well as other components such as enzyme substrates, chaperones, artificial amino acids, or labeling molecules. Here we describe procedures for the production of recombinant proteins in the ALiCE (Almost Living Cell-free Expression) system, a lysate derived from tobacco cell suspension cultures that can be used to manufacture protein products for molecular and biochemical analysis as well as applications in the pharmaceutical industry.

Involvement of CspC in response to diverse environmental stressors in Escherichia coli

The ability of Escherichia coli surviving a cold shock lies mainly with the induction of a few Csps termed as 'Major cold shock proteins'. Regardless of high sequence similarity among the nine homologous members, CspC appears to be functionally diverse in conferring the cell adaptability to various stresses based on fundamental properties of the protein including nucleic acid binding, nucleic acid melting and regulatory activity. Spanning three different stress regulons of acid, oxidative and heat, CspC regulates gene expression and transcript stability of stress proteins and bestows upon the cell tolerance to lethal-inducing agents ultimately helping it adapt to severe environmental assaults. While its exact role in cellular physiology is still to be detailed, understanding the transcriptional and translational control will likely provide insights into the mechanistic role of CspC under stress conditions. To this end, we review the knowledge on stress protein regulation by CspC and highlight its activity in response to stressors thereby elucidating its role as a major Csp player in response to one too many environmental triggers. The knowledge presented here could see various downstream applications in engineering microbes for industrial, agricultural and research applications in order to achieve high product efficiency and to aid bacteria cope with environmentally harsh conditions.

DiRect: Site-directed mutagenesis method for protein engineering by rational design

Site-directed mutagenesis (SDM), an indispensable method in molecular biology and protein engineering, is rather time-consuming and laborious. Protein engineering, especially that of enzymes, nowadays increasingly relies on rational design approaches in which both SDM and protein expression are the bottlenecks because they are generally based on the recombinant DNA technology. Here, we developed a new PCR-based mutagenesis method, DiRect, that achieves high performance in product quality (≥99% substitution) without recombinant DNA technology. We applied DiRect in combination with a cell-free protein expression system to an industrially relevant enzyme, nicotinamide adenine dinucleotide phosphate-dependent 3-quinuclidinone reductase from Rhodotorula rubra. In a single round of screening, 90 newly designed mutant proteins were produced within two days, and an unreported mutant (Q135I) exhibiting much higher thermostability than the wild-type enzyme was successfully identified within one extra day. Thus, DiRect is a simple, efficient, and potentially scalable SDM method.

Cell-Free Exploration of the Natural Product Chemical Space

Natural products and secondary metabolites comprise an indispensable resource from living organisms that have transformed areas of medicine, agriculture, and biotechnology. Recent advances in high-throughput DNA sequencing and computational analysis suggest that the vast majority of natural products remain undiscovered. To accelerate the natural product discovery pipeline, cell-free metabolic engineering approaches used to develop robust catalytic networks are being repurposed to access new chemical scaffolds, and new enzymes capable of performing diverse chemistries. Such enzymes could serve as flexible biocatalytic tools to further expand the unique chemical space of natural products and secondary metabolites, and provide a more sustainable route to manufacture these molecules. Herein, we highlight select examples of natural product biosynthesis using cell-free systems and propose how cell-free technologies could facilitate our ability to access and modify these structures to transform synthetic and chemical biology.