A global network-based protocol for functional inference of hypothetical proteins in Synechocystis sp. PCC 6803

Gao, Linfeng; Pei, Guangsheng; Chen, Lei; Zhang, Weiwen

doi:10.1016/j.mimet.2015.06.013

Cited by 5 publications

(3 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2 c). The high ratio of functionally unknown identified proteins is probably due to the fact that more than 33 % of proteins in the Synechocystis genome are hypothetical proteins [ 17 ]. Other frequently detected functional categories included “amino acid transport and metabolism” (8.62 %), “translation, ribosomal structure and biogenesis” (7.65 %), “cell wall/membrane/envelope biogenesis” (7.59 %), “energy production and conversion” (7.55 %) and “Signal transduction mechanisms” (6.79 %).…”

Section: Resultsmentioning

confidence: 99%

Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803

Wang

Chen

Zhang

2016

Biotechnol Biofuels

Self Cite

View full text Add to dashboard Cite

Background3-hydroxypropionic acid (3-HP) is an important platform chemical with a wide range of applications. In our previous study, the biosynthetic pathway of 3-HP was constructed and optimized in cyanobacterium Synechocystis sp. PCC 6803, which led to 3-HP production directly from CO2 at a level of 837.18 mg L−1 (348.8 mg/g dry cell weight). As the production and accumulation of 3-HP in cells affect cellular metabolism, a better understanding of cellular responses to 3-HP synthesized internally in Synechocystis will be important for further increasing 3-HP productivity in cyanobacterial chassis.ResultsUsing a engineered 3-HP-producing SM strain, in this study, the cellular responses to 3-HP internally produced were first determined using a quantitative iTRAQ-LC–MS/MS proteomics approach and a LC–MS-based targeted metabolomics. A total of 2264 unique proteins were identified, which represented about 63 % of all predicted protein in Synechocystis in the proteomic analysis; meanwhile intracellular abundance of 24 key metabolites was determined by a comparative metabolomic analysis of the 3-HP-producing strain SM and wild type. Among all identified proteins, 204 proteins were found up-regulated and 123 proteins were found down-regulated, respectively. The proteins related to oxidative phosphorylation, photosynthesis, ribosome, central carbon metabolism, two-component systems and ABC-type transporters were up-regulated, along with the abundance of 14 metabolites related to central metabolism. The results suggested that the supply of ATP and NADPH was increased significantly, and the precursor malonyl-CoA and acetyl-CoA may also be supplemented when 3-HP was produced at a high level in Synechocystis. Confirmation of proteomic and metabolomic results with RT-qPCR and gene-overexpression strains of selected genes was also conducted, and the overexpression of three transporter genes putatively involved in cobalt/nickel, manganese and phosphate transporting (i.e., sll0385, sll1598 and sll0679) could lead to an increased 3-HP production in Synechocystis.ConclusionsThe integrative analysis of up-regulated proteome and metabolome data showed that to ensure the high-efficient production of 3-HP and the normal growth of Synechocystis, multiple aspects of cells metabolism including energy, reducing power supply, central carbon metabolism, the stress responses and protein synthesis were enhanced in Synechocystis. The study provides an important basis for further engineering cyanobacteria for high 3-HP production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0627-6) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803

Wang

Chen

Zhang

2016

Biotechnol Biofuels

Self Cite

View full text Add to dashboard Cite

show abstract

“…CF-1 has revealed the existence of a very high number of genes with unknown function (1519 out of 2736; 56%), most of which are present in genetic contexts that are also unknown in terms of function [ 9 ]. These hypothetical genes have the regulatory elements required to be transcribed and translated, but the predicted products have no known function or structure, making their biological role and contribution towards adaptation to extreme life impossible to deduce [ 10 ]. In the case of strain CF-1, and other strains of the genus, more than half of the annotated genes in its genome still need to be functionally characterized.…”

Section: Introductionmentioning

confidence: 99%

“…This proportion is similar to less-characterized microorganisms or extremophiles (> 50%) [ 11 ], and substantially higher than in model organisms (25–40%; [ 12 ]. For example, in cyanobacterial genomes, 30–60% of the putative proteins are encoded by hypothetical genes depending on the species [ 10 ]. A similar profile has been described for extremophilic microorganisms; for example, 36% are hypothetical proteins in Acidithiobacillus ferrooxidans and At.…”

Section: Introductionmentioning

confidence: 99%

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

et al. 2022

View full text Add to dashboard Cite

Background Acidophilic microorganisms like Leptospirillum sp. CF-1 thrive in environments with extremely low pH and high concentrations of dissolved heavy metals that can induce the generation of reactive oxygen species (ROS). Several hypothetical genes and proteins from Leptospirillum sp. CF-1 are known to be up-regulated under oxidative stress conditions. Results In the present work, the function of hypothetical gene ABH19_09590 from Leptospirillum sp. CF-1 was studied. Heterologous expression of this gene in Escherichia coli led to an increase in the ability to grow under oxidant conditions with 5 mM K2CrO4 or 5 mM H2O2. Similarly, a significant reduction in ROS production in E. coli transformed with a plasmid carrying ABH19_09590 was observed after exposure to these oxidative stress elicitors for 30 min, compared to a strain complemented with the empty vector. A co-transcriptional study using RT-PCR showed that ABH19_09590 is contained in an operon, here named the “och” operon, that also contains ABH19_09585, ABH19_09595 and ABH19_09600 genes. The expression of the och operon was significantly up-regulated in Leptospirillum sp. CF-1 exposed to 5 mM K2CrO4 for 15 and 30 min. Genes of this operon potentially encode a NADH:ubiquinone oxidoreductase, a CXXC motif-containing protein likely involved in thiol/disulfide exchange, a hypothetical protein, and a di-hydroxy-acid dehydratase. A comparative genomic analysis revealed that the och operon is a characteristic genetic determinant of the Leptospirillum genus that is not present in other acidophiles. Conclusions Altogether, these results suggest that the och operon plays a protective role against chromate and hydrogen peroxide and is an important mechanism required to face polyextremophilic conditions in acid environments.

show abstract

Direct Photosynthetic Production of Plastic Building Block Chemicals from CO2

Song

Wang

Diao

et al. 2018

Advances in Experimental Medicine and Biology

View full text Add to dashboard Cite

Hydroxy acids have attracted attention as building block chemicals due to their roles as precursors for the production of various pharmaceuticals, vitamins, antibiotics, and flavor compounds as well as monomers for biodegradable plastic polyesters. The current approach to hydroxy acid production relies on nonrenewable fossil resources such as petroleum for raw materials, raising issues such as the rising costs of starting materials and environmental incompatibility. Recently, synthetic biology approaches based on the rational design and reconstruction of new biological systems were implemented to produce chemicals from a variety of renewable substrates. In addition to research using heterotrophic organic carbon-dependent Escherichia coli or yeasts, photosynthetic microorganisms such as cyanobacteria possessing the ability to absorb solar radiation and fix carbon dioxide (CO) as a sole carbon source have been engineered into a new type of microbial cell factory to directly produce hydroxy acids from CO. In this chapter, recent progress regarding the direct photosynthetic production of three important hydroxy acids-3-hydroxypropionate (3-HP), 3-hydroxybutyrate (3-HB), and 3-hydroxyvalerate (3-HV)-from CO in cyanobacteria is summarized and discussed.

show abstract

A global network-based protocol for functional inference of hypothetical proteins in Synechocystis sp. PCC 6803

Cited by 5 publications

References 74 publications

Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803

Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

Direct Photosynthetic Production of Plastic Building Block Chemicals from CO2

Contact Info

Product

Resources

About