Genome shuffling leads to rapid phenotypic improvement in bacteria

Zhang, Yingxin; Perry, Kim; Vinci, Victor A.; Powell, Keith A.; Stemmer, Willem P.C.; Cardayré, Stephen B. del

doi:10.1038/415644a

Cited by 521 publications

(304 citation statements)

References 13 publications

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“…A straightforward approach would be to select or screen for strains with improved robustness to lignocellulose hydrolysate. Combining the best properties of the currently available strains could potentially be achieved by enhanced breeding techniques (Zhang et al, 2002) or through the identification of the molecular basis of certain desirable features (Sonderegger et al, 2004;van Maris et al, 2004) and inverse metabolic engineering . Table IV.…”

Section: Discussionmentioning

confidence: 99%

Fermentation performance of engineered and evolved xylose‐fermenting Saccharomyces cerevisiae strains

Sonderegger

Jeppsson

Larsson

et al. 2004

Biotech & Bioengineering

130

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Lignocellulose hydrolysate is an abundant substrate for bioethanol production. The ideal microorganism for such a fermentation process should combine rapid and efficient conversion of the available carbon sources to ethanol with high tolerance to ethanol and to inhibitory components in the hydrolysate. A particular biological problem are the pentoses, which are not naturally metabolized by the main industrial ethanol producer Saccharomyces cerevisiae. Several recombinant, mutated, and evolved xylose fermenting S. cerevisiae strains have been developed recently. We compare here the fermentation performance and robustness of eight recombinant strains and two evolved populations on glucose/xylose mixtures in defined and lignocellulose hydrolysate-containing medium. Generally, the polyploid industrial strains depleted xylose faster and were more resistant to the hydrolysate than the laboratory strains. The industrial strains accumulated, however, up to 30% more xylitol and therefore produced less ethanol than the haploid strains. The three most attractive strains were the mutated and selected, extremely rapid xylose consumer TMB3400, the evolved C5 strain with the highest achieved ethanol titer, and the engineered industrial F12 strain with by far the highest robustness to the lignocellulosic hydrolysate. B

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Section: Discussionmentioning

confidence: 99%

Fermentation performance of engineered and evolved xylose‐fermenting Saccharomyces cerevisiae strains

Sonderegger

Jeppsson

Larsson

et al. 2004

Biotech & Bioengineering

130

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“…Much of what is known empirically about the effects of recombination in systems where the genotype-phenotype relationship is complex stems from the gene and protein level. Although recombination is more frequent on levels of organization above the molecule (Zhang et al 2002), we know much less about its effects on these important levels. In particular, there have been relatively few studies of the effects of recombination on gene circuits, i.e., groups of genes that jointly perform a biological task.…”

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confidence: 99%

Effects of Recombination on Complex Regulatory Circuits

Martin

Wagner

2009

Genetics

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Mutation and recombination are the two main forces generating genetic variation. Most of this variation may be deleterious. Because recombination can reorganize entire genes and genetic circuits, it may have much greater consequences than point mutations. We here explore the effects of recombination on models of transcriptional regulation circuits that play important roles in embryonic development. We show that recombination has weaker deleterious effects on the expression phenotypes of these circuits than mutations. In addition, if a population of such circuits evolves under the influence of mutation and recombination, we find that three key properties emerge: (1) deleterious effects of mutations are reduced dramatically; (2) the diversity of genotypes in the population is greatly increased, a feature that may be important for phenotypic innovation; and (3) cis-regulatory complexes appear. These are combinations of regulatory interactions that influence the expression of one gene and that mitigate deleterious recombination effects.

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“…In addition, the severe phenotype of CD28-and CTLA-4-deficient mice (4,5,8,(12)(13)(14) and the structurally conserved ligand binding sites of CD80 and CD86 (20 -24) suggest that natural evolution has strongly favored the binding of B7 molecules to both of their respective ligands. Directed molecular evolution by DNA shuffling followed by screening has previously been successful in evolving, for example, subtilisin, interferon ␣, viruses, and bacteria (25)(26)(27)(28)(29)(30)(31). We hypothesized that directed molecular evolution of diverse mammalian CD80 genes by DNA shuffling combined with the appropriate screening procedures would enable the generation of chimeric molecules that preferentially bind and signal through either CD28 or CTLA-4.…”

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confidence: 99%

Chimeric Co-stimulatory Molecules That Selectively Act through CD28 or CTLA-4 on Human T Cells

Lazetic

Leong

Chang

et al. 2002

Journal of Biological Chemistry

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CD28 and CTLA-4 (CD152) play a pivotal role in the regulation of T cell activation. Upon ligation by CD80 (B7-1) or CD86 (B7-2), CD28 induces T cell proliferation, cytokine production, and effector functions, whereas CTLA-4 signaling inhibits expansion of activated T cells and induces tolerance. Therefore, we hypothesized that co-stimulatory molecules that preferentially bind CD28 or CTLA-4 would have dramatically altered biological properties. We describe directed molecular evolution of CD80 genes derived from human, orangutan, rhesus monkey, baboon, cat, cow, and rabbit by DNA shuffling and screening. In contrast to wild-type CD80, the evolved co-stimulatory molecules, termed CD28-binding protein (CD28BP) and CTLA-4-binding protein (CTLA-4BP), selectively bind to CD28 or CTLA-4, respectively. Furthermore, CD28BP has improved capacity to induce human T cell proliferation and interferon-␥ production compared with wild-type CD80. In contrast, CTLA-4BP inhibited human mixed leukocyte reaction (MLR) and enhanced interleukin 10 production in MLR, supporting a role for CTLA-4BP in inducing T cell anergy and tolerance. In addition, co-stimulation of purified human T cells was significantly suppressed when CTLA-4BP was cotransfected with either CD80 or CD28BP. The amino acid sequences of CD28BP and CTLA-4BP were 61 and 96% identical with that of human CD80 and provide insight into the residues that are critical in the ligand binding. These molecules provide a new approach to characterization of CD28 and CTLA-4 signals and to manipulation of the T cell response.T cell response is dependent on complex integration of antigen-specific and nonspecific extracellular and intracellular signals. The specificity of the response is determined by recognition of an antigenic peptide in the context of major histocompatibility complex on the plasma membrane of antigen-presenting cells, such as monocytes, dendritic cells, Langerhans cells, or primed B cells. However, a second signal, mediated by co-stimulatory molecules expressed on antigenpresenting cells, is required for induction of a complete T cell response (1-3). The most extensively studied co-stimulatory molecules are CD80 (B7-1) and CD86 (B7-2), which bind the CD28 and CTLA-4 (CD152) ligands expressed on CD4 ϩ and CD8 ϩ T cells. Additional co-stimulatory molecule-ligand pairs such as ICOS-B7-H and PD1-PDL have recently been identified, further illustrating the complexity of the signals that regulate the function of T cells (1-3). Co-stimulatory signal in addition to the T cell receptor signal is a prerequisite for induction of optimal T activation, proliferation, cytokine production, and effector functions.The functional characterization of CD80, CD86, CD28, and CTLA-4 has also illustrated the delicate balance between positive and negative signals mediated through CD28 and CTLA-4, respectively. Upon ligation by CD80 or CD86, CD28 synergizes with T cell receptor signaling to induce activation of both CD4 ϩ and CD8 ϩ T cells (4 -7), whereas CTLA-4 ligation inhibits expansion of...

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Genome shuffling leads to rapid phenotypic improvement in bacteria

Cited by 521 publications

References 13 publications

Fermentation performance of engineered and evolved xylose‐fermenting Saccharomyces cerevisiae strains

Fermentation performance of engineered and evolved xylose‐fermenting Saccharomyces cerevisiae strains

Effects of Recombination on Complex Regulatory Circuits

Chimeric Co-stimulatory Molecules That Selectively Act through CD28 or CTLA-4 on Human T Cells

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