Dataset Information

Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters.

ABSTRACT: Precise regulation of gene expression is fundamental for tailor-made gene circuit design in synthetic biology. Current strategies for this type of development are mainly based on directed evolution beginning with a native promoter template. The performances of engineered promoters are usually limited by the growth phase because only one promoter is recognized by one type of sigma factor (?). Here, we constructed multiple-? recognizable artificial hybrid promoters (AHPs) composed of tandems of dual and triple natural minimal promoters (NMPs). These NMPs, which use ?A, ?H and ?W, had stable functions in different growth phases. The functions of these NMPs resulted from an effect called transcription compensation, in which AHPs sequentially use one type of ? in the corresponding growth phase. The strength of the AHPs was influenced by the combinatorial order of each NMP and the length of the spacers between the NMPs. More importantly, the output of the precise regulation was achieved by equipping AHPs with synthetic ribosome binding sites and by redesigning them for induced systems. This strategy might offer promising applications to rationally design robust synthetic promoters in diverse chassis to spur the construction of more complex gene circuits, which will further the development of synthetic biology.

SUBMITTER: Han L

PROVIDER: S-EPMC7042180 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters.

Han Laichuang L Chen Qiaoqing Q Lin Qiao Q Cheng Jintao J Zhou Li L Liu Zhongmei Z Guo Junling J Zhang Linpei L Cui Wenjing W Zhou Zhemin Z

Frontiers in bioengineering and biotechnology 20200219

Precise regulation of gene expression is fundamental for tailor-made gene circuit design in synthetic biology. Current strategies for this type of development are mainly based on directed evolution beginning with a native promoter template. The performances of engineered promoters are usually limited by the growth phase because only one promoter is recognized by one type of sigma factor (σ). Here, we constructed multiple-σ recognizable artificial hybrid promoters (AHPs) composed of tandems of du ...[more]

PMID: 32140461

Similar Datasets

Project description:Development of robust and efficient methods for analyzing and interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports the assumption that genes express and perform their functions in modular fashions in cells. Therefore, there is an open space for development of the timely and relevant computational algorithms that use robust functional expression profiles towards precise classification of complex human diseases at the modular level.Inspired by the insight that genes act as a module to carry out a highly integrated cellular function, we thus define a low dimension functional expression profile for data reduction. After annotating each individual gene to functional categories defined in a proper gene function classification system such as Gene Ontology applied in this study, we identify those functional categories enriched with differentially expressed genes. For each functional category or functional module, we compute a summary measure (s) for the raw expression values of the annotated genes to capture the overall activity level of the module. In this way, we can treat the gene expressions within a functional module as an integrative data point to replace the multiple values of individual genes. We compare the classification performance of decision trees based on functional expression profiles with the conventional gene expression profiles using four publicly available datasets, which indicates that precise classification of tumour types and improved interpretation can be achieved with the reduced functional expression profiles.This modular approach is demonstrated to be a powerful alternative approach to analyzing high dimension microarray data and is robust to high measurement noise and intrinsic biological variance inherent in microarray data. Furthermore, efficient integration with current biological knowledge has facilitated the interpretation of the underlying molecular mechanisms for complex human diseases at the modular level.

Project description:Despite the remarkable advances in behavioral and brain sciences over the last decades, the mind-body (brain) problem is still an open debate and one of the most intriguing questions for both cognitive neuroscience and philosophy of mind. Traditional approaches have conceived this problem in terms of a contrast between physicalist monism and Cartesian dualism. However, since the late sixties, the landscape of philosophical views on the problem has become more varied and complex. The Multiple Realization Thesis (MRT) claims that mental properties can be (or are) realized, and mental processes can be (or are) implemented by neural correlates of different kinds. Thus, MRT challenges the psychoneural type-identity theory and the corresponding reductionism. Many philosophers have acknowledged the a priori plausibility of MRT. However, the existence of empirical evidence in favor of intraspecific, human multiple realizations of mental processes and properties is still controversial. Here, we illustrate some cases that provide empirical evidence in support of MRT. Recently, it has been proposed that foveal agnosic vision, like peripheral vision, can be restored by increasing object parts' spacing (Crutch and Warrington, 2007; Strappini et al., 2017b). Agnosic fovea and normal periphery are both limited by crowding, which impairs object recognition, and provides the signature of visual integration. Here, we define a psychological property of restored object identification, and we cross-reference the data of visually impaired patients with different etiologies. In particular, we compare the data of two stroke patients, two patients with posterior cortical atrophy, six cases of strabismic amblyopia, and one case with restored sight. We also compare these patients with unimpaired subjects tested in the periphery. We show that integration (i.e., restored recognition) seems to describe quite accurately the visual performance in all these cases. Whereas the patients have different etiologies and different neural correlates, the unimpaired subjects have no neural damage. Thus, similarity in the psychological property given the differences in the neural substrate can be interpreted in relation to MRT and provide evidence in its support. Finally, we will frame our contribution within the current debate concerning MRT providing new and compelling empirical evidence.

Dataset Information

Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters.

Publications

Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets