A bacterial homolog YciH of eukaryotic translation initiation factor eIF1 regulates stress-related gene expression and is unlikely to be involved in translation initiation fidelity

Osterman, Ilya А.; Evfratov, Sergey; Dzama, Margarita M.; Pletnev, Philipp; Kovalchuk, Sergey I.; Butenko, Ivan; Pobeguts, Olga; Golovina, Anna Y.; Govorun, Vadim M.; Bøgdanov, A.; Сергиев, Петр В.; Dontsova, Olga А.

doi:10.1080/15476286.2015.1069464

Cited by 8 publications

(6 citation statements)

References 28 publications

(38 reference statements)

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“…Polar effects due to CRISPRi inhibition of pyrF resulted in significant downregulation of YciH protein levels (Table S5). Knock-out of yciH has previously been shown to increase expression of 66 genes, and decrease expression of 20 genes in E. coli (Osterman et al, 2015); however, none of these proteins were found to be significantly up-or downregulated in our study. Polar effects of pyrG inhibition resulted in the downregulation of eno, located downstream of pyrG (Table S5).…”

Section: Polar Effectscontrasting

confidence: 89%

CRISPR interference of nucleotide biosynthesis improves production of a single‐domain antibody in Escherichia coli

Landberg

Wright

Wulff

et al. 2020

Biotech & Bioengineering

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Growth decoupling can be used to optimize the production of biochemicals and proteins in cell factories. Inhibition of excess biomass formation allows for carbon to be utilized efficiently for product formation instead of growth, resulting in increased product yields and titers. Here, we used CRISPR interference to increase the production of a single-domain antibody (sdAb) by inhibiting growth during production. First, we screened 21 sgRNA targets in the purine and pyrimidine biosynthesis pathways and found that the repression of 11 pathway genes led to the increased green fluorescent protein production and decreased growth. The sgRNA targets pyrF, pyrG, and cmk were selected and further used to improve the production of two versions of an expression-optimized sdAb. Proteomics analysis of the sdAbproducing pyrF, pyrG, and cmk growth decoupling strains showed significantly decreased RpoS levels and an increase of ribosome-associated proteins, indicating that the growth decoupling strains do not enter stationary phase and maintain their capacity for protein synthesis upon growth inhibition. Finally, sdAb production was scaled up to shake-flask fermentation where the product yield was improved 2.6-fold compared to the control strain with no sgRNA target sequence. An sdAb content of 14.6% was reached in the best-performing pyrG growth decoupling strain.

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Section: Polar Effectscontrasting

confidence: 89%

CRISPR interference of nucleotide biosynthesis improves production of a single‐domain antibody in Escherichia coli

Landberg

Wright

Wulff

et al. 2020

Biotech & Bioengineering

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“…Among a few other translation initiation factors, eIF1 is considered to be universally conserved in all the three domains of life; however, the homologue of eIF1, known as YciH, is not present in all bacteria . Furthermore, recent studies have revealed that instead of functioning as a translation initiation factor, YciH acts as an inhibitor of translation initiation during stress conditions by binding firmly to the P site with the aid of a longer β 1 –β 2 basic loop . The fidelity of translation initiation in bacteria is alternatively established by the initiation factor IF3; which, however, lacks sequence or structural homology with the protein eIF1 .…”

mentioning

confidence: 99%

Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops

Gogoi

Kanaujia

2018

FEBS Letters

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The archaeal translation initiation factor 1 (aIF1) is reported to be functionally homologous to the eukaryotic translation initiation factor 1 (eIF1). However, lack of a structural comparison between aIF1 and eIF1 has limited our understanding of the structural (dis)similarities. Herein, we have determined the three-dimensional crystal structure of an open reading frame PH1771.1 encoding aIF1 in Pyrococcus horikoshii OT3. Results reveal that although aIF1 has low sequence similarity with eIF1, high structural homology exists between the two proteins. Nonetheless, notable critical differences between aIF1 and eIF1 could still be perceived at the β -β basic loop, the acidic loop and the solvent-exposed surface. These differences might lead to a slightly divergent mode of action of aIF1 during archaeal translation initiation.

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“…The bacterial cells were suspended as described in [21]. The LC-MS was performed on a TripleTOF 5600+ (Sciex, USA) mass-spectrometer operating in in a data-dependent mode with a NanoSpray III ion source (Sciex, USA) coupled to a NanoLC Ultra 2D+ nano-HPLC system (Eksigent, USA) configured as described in [22].…”

Section: Methodsmentioning

confidence: 99%

Large scale analysis of amino acid substitutions in bacterial proteomics

et al. 2016

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BackgroundProteomics of bacterial pathogens is a developing field exploring microbial physiology, gene expression and the complex interactions between bacteria and their hosts. One of the complications in proteomic approach is micro- and macro-heterogeneity of bacterial species, which makes it impossible to build a comprehensive database of bacterial genomes for identification, while most of the existing algorithms rely largely on genomic data.ResultsHere we present a large scale study of identification of single amino acid polymorphisms between bacterial strains. An ad hoc method was developed based on MS/MS spectra comparison without the support of a genomic database. Whole-genome sequencing was used to validate the accuracy of polymorphism detection. Several approaches presented earlier to the proteomics community as useful for polymorphism detection were tested on isolates of Helicobacter pylori, Neisseria gonorrhoeae and Escherichia coli.ConclusionThe developed method represents a perspective approach in the field of bacterial proteomics allowing to identify hundreds of peptides with novel SAPs from a single proteome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1301-5) contains supplementary material, which is available to authorized users.

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A bacterial homolog YciH of eukaryotic translation initiation factor eIF1 regulates stress-related gene expression and is unlikely to be involved in translation initiation fidelity

Cited by 8 publications

References 28 publications

CRISPR interference of nucleotide biosynthesis improves production of a single‐domain antibody in Escherichia coli

CRISPR interference of nucleotide biosynthesis improves production of a single‐domain antibody in Escherichia coli

Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops

Large scale analysis of amino acid substitutions in bacterial proteomics

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