Metabolic and evolutionary engineering research in Turkey and beyond

Abstract

This review discusses metabolic engineering research with an emphasis on evolutionary (whole cell and protein) engineering, which is an inverse metabolic engineering approach. For each section on metabolic, inverse metabolic and evolutionary engineering research, a general review of the major global studies in the literature is made and research examples from Turkey are given and discussed. It is expected that with the rapid development in systems biology and the novel powerful analytical technologies to identify the genetic basis of cellular phenotypes, metabolic and evolutionary engineering research will become widespread and increasingly important in Turkey, following global scientific trends.

Technological trends, global market, and challenges of bio-ethanol production

“…In addition, the so-called conventional methodologies of mutagenesis and screening are still very useful in microbial improvement programs (Parekh et al, 2000). The combination of such tools with evolutionary engineering strategies (Çakar, 2009;Sauer, 2001) constitutes a powerful approach for the improvement of strains in the specific harsh environments typical of certain industrial fermentation processes. More recently, novel approaches have been devised and applied to improve ethanol production by S. cerevisiae, particularly genome shuffling (Shi et al, 2009;Hou, 2009) and global transcription machinery engineering (gTME) (Alper et al, 2006).…”

Production of L‐DOPA and dopamine in recombinant bacteria bearing the Vitreoscilla hemoglobin gene

“…Indeed, the term "metabolic engineering" was first used in association with VHb [11]. In a review article in this issue of the Journal, Z. P. Çakar gives an overview on metabolic and evolutionary engineering research and VHb, one of the foremost examples of metabolic engineering [12]. The VHb was the first prokaryotic hemoglobin to be characterized in detail [13][14][15][16][17][18][19] and since its discovery in late 1980s, the Vitreoscilla hemoglobin gene (vgb) has been cloned and expressed in various heterologous organisms including animals [20], plants [21][22][23][24][25][26][27], fungi [28][29][30][31][32][33] and other bacteria to enhance growth, productivity and other certain activities, especially under restricted oxygen conditions.…”

The application of microfluidic-based technologies in the cycle of metabolic engineering

“…This can rapidly reveal significant differences in the gene transcription level among individual cells, aiding parallel validation of the efforts in modifying targeted genes. The comparative analysis of genome and transcriptome among different cells helps to identify the key genetic factors that endow the desired phenotypes, facilitating directed manipulation of other strains in the process of inverse metabolic engineering [37] . Moreover, the single-cell omic analysis captures a “snap-shot” of the cell status, a series of “snap-shots” will create a dynamic record of the cellular metabolism, offering timing and causal analysis of the metabolic regulation mechanisms.…”