Optimization of carbon and energy utilization through differential translational efficiency

Al‐Bassam, Mahmoud M.; Kim, Ji-Nu; Zaramela, Livia S.; Kellman, Benjamin P.; Zuñiga, Cristal; Wozniak, Jacob M.; Gonzalez, David J.; Zengler, Karsten

doi:10.1038/s41467-018-06993-6

Cited by 40 publications

(65 citation statements)

References 69 publications

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“…This phenomenon has been observed during evolution 18 , development 19 , differentiation 20,21 , cell-type specificity 22 , circadian regulation 23 , and stress adaptation 14,[24][25][26][27][28][29][30][31] . This raises the question as to the identity of translatome remodelers that target different mRNA populations to bring about global, stimuli-induced translatome reprogramming 25,32 , especially in response to physiological stimuli e.g., hypoxia [33][34][35] . Recent work indicates that adaptive translatome remodeling is driven by specialized translation machineries 36,37 , such as the hypoxic cap-binding complex eIF4F H (consisting of eIF4E2 38 and eIF4G3) 25,39 , eIF4E3 40 , eIF3d 37 , DAP5 41,42 , and eIF5B 43 .…”

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confidence: 99%

A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism

Balukoff

Theodoridis

et al. 2020

Nat Commun

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Protein expression evolves under greater evolutionary constraint than mRNA levels, and translation efficiency represents a primary determinant of protein levels during stimuli adaptation. This raises the question as to the translatome remodelers that titrate protein output from mRNA populations. Here, we uncover a network of RNA-binding proteins (RBPs) that enhances the translation efficiency of glycolytic proteins in cells responding to oxygen deprivation. A system-wide proteomic survey of translational engagement identifies a family of oxygen-regulated RBPs that functions as a switch of glycolytic intensity. Tandem mass tagpulse SILAC (TMT-pSILAC) and RNA sequencing reveals that each RBP controls a unique but overlapping portfolio of hypoxic responsive proteins. These RBPs collaborate with the hypoxic protein synthesis apparatus, operating as a translation efficiency checkpoint that integrates upstream mRNA signals to activate anaerobic metabolism. This system allows anoxiaresistant animals and mammalian cells to initiate anaerobic glycolysis and survive hypoxia. We suggest that an oxygen-sensitive RBP cluster controls anaerobic metabolism to confer hypoxia tolerance.

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confidence: 99%

A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism

Balukoff

Theodoridis

et al. 2020

Nat Commun

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“…Through transcriptome analysis, it was possible to reveal the level of transcriptional expression of genes related to the WL pathway and the energy conservation system in acetogens under autotrophic conditions [ 36 , 105 , 106 , 107 , 108 , 109 , 110 ]. In addition, ribosome profiling in C. ljungdahlii or E. limosum revealed that translational regulation of genes in the carbonyl-branch or energy conservation system is critical to their autotrophic growth [ 111 , 112 ]. Recently, a genome-scale metabolic model (GEM) has been constructed for C. ljungdahlii , C. autoethanogenum , and C. drakei ( Table 4 ).…”

Section: Synthetic Biology Approach On Acetogensmentioning

confidence: 99%

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

Jin

Bae

Song

et al. 2020

IJMS

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Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.

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“…These models have been successfully validated as a systems biology framework and deployed for a variety of uses. For example, models have been utilized for elucidating fundamental metabolic processes [23][24][25][26] , optimizing culture media and growth conditions 27,28 , and have been essential for metabolic engineering efforts 29 . These metabolic models are genome-scale knowledge databases, which contain manually curated annotation related to gene-proteinreaction associations for all possible metabolic reactions inside a cell.…”

Section: Introductionmentioning

confidence: 99%

“…These metabolic models are genome-scale knowledge databases, which contain manually curated annotation related to gene-protein-reaction associations for all possible metabolic reactions inside a cell. Reconstructed models have been used to understand and channel the metabolism of different pathogenic and non-pathogenic microorganisms 16 , 30 , as well as to contextualize metabolic states based on omics data 24 . Here, we reconstructed genome-scale models for seven Liberibacter strains and evaluated their physiology and metabolic response.…”

Section: Introductionmentioning

confidence: 99%

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Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

et al. 2020

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Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.

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Optimization of carbon and energy utilization through differential translational efficiency

Cited by 40 publications

References 69 publications

A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism

A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

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