Use of transcriptomic data for extending a model of the AppA/PpsR system in Rhodobacter sphaeroides

Pandey, R.; Armitage, Judith P.; Wadhams, George H.

doi:10.1186/s12918-017-0489-y

Cited by 6 publications

(4 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this sense, BlsA probes to be unique among described photoreceptors regarding its dual activity under illumination and in the dark. Indeed, many photoreceptors have been shown to antagonize transcriptional repressors (Tuttobene et al, 2018), such as AppA from Rhodobacter sphaeroides (Pandey et al, 2017), PixD from Synechocystis sp. PCC6803 (Fujisawa and Masuda, 2017), and YcgF from E. coli (Tschowri et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp.

et al. 2019

View full text Add to dashboard Cite

Acinetobacter spp. are found in all environments on Earth due to their extraordinary capacity to survive in the presence of physical and chemical stressors. In this study, we analyzed global gene expression in airborne Acinetobacter sp. strain 5-2Ac02 isolated from hospital environment in response to quorum network modulators and found that they induced the expression of genes of the acetoin/butanediol catabolism, volatile compounds shown to mediate interkingdom interactions. Interestingly, the acoN gene, annotated as a putative transcriptional regulator, was truncated in the downstream regulatory region of the induced acetoin/butanediol cluster in Acinetobacter sp. strain 5-2Ac02, and its functioning as a negative regulator of this cluster integrating quorum signals was confirmed in Acinetobacter baumannii ATCC 17978. Moreover, we show that the acetoin catabolism is also induced by light and provide insights into the light transduction mechanism by showing that the photoreceptor BlsA interacts with and antagonizes the functioning of AcoN in A. baumannii , integrating also a temperature signal. The data support a model in which BlsA interacts with and likely sequesters AcoN at this condition, relieving acetoin catabolic genes from repression, and leading to better growth under blue light. This photoregulation depends on temperature, occurring at 23°C but not at 30°C. BlsA is thus a dual regulator, modulating different transcriptional regulators in the dark but also under blue light, representing thus a novel concept. The overall data show that quorum modulators as well as light regulate the acetoin catabolic cluster, providing a better understanding of environmental as well as clinical bacteria.

show abstract

Section: Discussionmentioning

confidence: 99%

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp.

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Ultimately, important knowledge has been obtained from fundamental studies on photosynthetic gene regulation and physiology (Gomelsky et al, 2008; Moskvin et al, 2005; Pappas et al, 2004; Zeilstra‐Ryalls & Kaplan, 2004). This was further combined in a model for describing the effect of oxygen availability on the expression of photosynthetic genes (Pandey et al, 2017). All this knowledge can be applied for, for example, improving isoprenoid or H 2 production under different growth modes.…”

Section: Different Research Fields Contributed To the Dbtl Methods In mentioning

confidence: 99%

“…This building phase largely benefited from recent advancements, rendering genome editing in R. sphaeroides easier to implement. In particular, they allowed successful genomic manipulations ranging from single nucleotide substitutions (Luo et al, 2020;Mougiakos et al, 2019) to entire pathway integration (Orsi, Beekwilder, Peek, et al, 2020 (Imam et al, 2011(Imam et al, , 2013, Oxygenresponse model (Pandey et al, 2017) Electroporation (Jun et al, 2014;Luo et al, 2020;Serdyuk et al, 2013), suicide plasmid-mediated genome editing (Jaschke et al, 2011), and BioBricks™ (Tikh et al, 2014) Transcriptomics and growth modes (Arai et al, 2008;Imam et al, 2014;Pappas et al, 2004) Genes regulation and physiological behavior (Arai et al, 2008;Moskvin et al, 2005;Pandey et al, 2017;Pappas et al, 2004;Zeilstra-Ryalls & Kaplan 1995 Quorum sensing Mutant library (Hwang & Lee, 2008) Genes regulation and physiological behavior (Hwang & Lee, 2008) Tools development…”

Section: Buildmentioning

confidence: 99%

The transition of Rhodobacter sphaeroides into a microbial cell factory

Orsi

Beekwilder²,

Eggink

et al. 2020

Biotech & Bioengineering

View full text Add to dashboard Cite

Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.

show abstract

“…More precisely, at high oxygen tension PpsR inhibits synthesis of bchl (bacteriochlorophylls) and crt (carotenoids) biosynthetic operons, while AppA acts at low oxygen tensions as derepressor on PpsR. Integration of the knowledge from these regulatory studies allowed to get a better comprehension on the physiology of R. sphaeroides while transitioning between aerobic and photosynthetic growth (74,75). These oxygen-dependent regulatory networks revealed to be involved also in morphological changes in R. sphaeroides.…”

Section: Towards Non-traditional Microbial Platforms For Isoprenoid Smentioning

confidence: 99%

Racing-red chassis : Advancing Rhodobacter sphaeroides as platform for isoprenoid production

Orsi¹

View full text Add to dashboard Cite

Diminishing the turnaround time of DBTL cycles is a crucial aspect for accelerating the development of microbial chassis (31, 32). Cutting edge advances in fields like systems biology (33), machine learning (34), metabolomics (35), automation (31), or genome engineering (36-38) can contribute to accelerate one or more parts of the DBTL cycle. Biofoundries have been realized, in which automated and high-throughput DBTL cycles are integrated for rapidly and efficiently reprogramming cell factories (31, 39). While rapid and standardized DBTL cycles can be performed for model organisms like E. coli or S. cerevisiae, their use for non-model microorganisms is not trivial (15). For example, potentially interesting chassis might lack genetic accessibility, which would render the 'build' phase cumbersome. Also, the metabolic pathways supporting product formation could be unknown. Therefore, implementation of DBTL cycles in non-traditional microorganisms is an intriguing challenge for biotechnology. Succeeding in such a task would allow to investigate and assess non-traditional microorganisms as potential cell factories. Isoprenoid compounds: a successful example for the bioeconomy obtained via DBTL cycles The case of semi-synthetic artemisinin synthesis in yeast Probably the most scientifically relevant achievement obtained via DBTL cycles is the microbial synthesis of the antimalarial drug artemisinin (40). Such a compound is natively produced by the plant Artemisia annua, but dependence on yearly harvesting makes its production challenging (41). Therefore, alternatives like microbial synthesis were explored for feasible and costcompetitive artemisinin production (40, 41). This endeavour started with the implementation of a heterologous production pathway in E. coli (42), and was concluded a decade later by producing up to 25 g/L of artemisinic acid in Fld/Fd red Fld/Fd ox

show abstract

Use of transcriptomic data for extending a model of the AppA/PpsR system in Rhodobacter sphaeroides

Cited by 6 publications

References 43 publications

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp.

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp.

The transition of Rhodobacter sphaeroides into a microbial cell factory

Racing-red chassis : Advancing Rhodobacter sphaeroides as platform for isoprenoid production

Contact Info

Product

Resources

About