Codon Bias Can Determine Sorting of a Potassium Channel Protein

Engel, Anja J.; Kithil, Marina; Langhans, Markus; Rauh, Oliver; Cartolano, Matea; Etten, James L. Van; Moroni, Anna; Thiel, Gerhard

doi:10.3390/cells10051128

Cited by 8 publications

(18 citation statements)

References 54 publications

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“…It has been described that codon optimization results in increased sorting of viral potassium channels to mitochondria. This seemed to be valid for several cell lines which suggests a general mechanism ( Engel et al, 2021 ). Therefore, this line of research seems very interesting, especially when considering that different potassium channels may be present in the mitochondria of different tissues.…”

Section: Introductionmentioning

confidence: 69%

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Current Challenges of Mitochondrial Potassium Channel Research

Kulawiak

Szewczyk

2022

Front. Physiol.

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In this paper, the current challenges of mitochondrial potassium channels research were critically reviewed. Even though recent progress in understanding K+ traffic in mitochondria has been substantial, some basic issues of this process remain unresolved. Here, we focused on the critical discussion of the molecular identity of various mitochondrial potassium channels. This point helps to clarify why there are different potassium channels in specific mitochondria. We also described interactions of mitochondrial potassium channel subunits with other mitochondrial proteins. Posttranslational modifications of mitochondrial potassium channels and their import are essential but unexplored research areas. Additionally, problems with the pharmacological targeting of mitochondrial potassium channel were illustrated. Finally, the limitation of the techniques used to measure mitochondrial potassium channels was explained. We believe that recognizing these problems may be interesting for readers but will also help to progress the field of mitochondrial potassium channels.

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Section: Introductionmentioning

confidence: 69%

“…Another interesting observation is that codon bias can alter the sorting of virus potassium channels between mitochondria and other cellular compartments ( Engel et al, 2021 ). It has been described that codon optimization results in increased sorting of viral potassium channels to mitochondria.…”

Section: Introductionmentioning

confidence: 99%

Current Challenges of Mitochondrial Potassium Channel Research

Kulawiak

Szewczyk

2022

Front. Physiol.

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“…There were differences between R5421 and THY.AP4 in genotype ( Grefen et al, 2009 ; Li et al, 2014 ). Codon bias affects proteins’ expression level, localization, time rhythm, and function ( Zhou et al, 2013 ; Engel et al, 2021 ). Grefen et al have optimized the codons of AKT1 of Arabidopsis and transferred it into THY.AP4 yeast to get better protein expression ( Grefen and Blatt, 2012 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of Shaker K+ Channel Gene Family in Foxtail Millet (Setaria italica) and Their Role in Stress Response

et al. 2022

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Potassium (K+) is one of the indispensable elements in plant growth and development. The Shaker K+ channel protein family is involved in plant K+ uptake and distribution. Foxtail millet (Setaria italica), as an important crop, has strong tolerance and adaptability to abiotic stresses. However, no systematic study focused on the Shaker K+ channel family in foxtail millet. Here, ten Shaker K+ channel genes in foxtail millet were identified and divided into five groups through phylogenetic analysis. Gene structures, chromosome locations, cis-acting regulatory elements in promoter, and post-translation modification sites of Shaker K+ channels were analyzed. In silico analysis of transcript level demonstrated that the expression of Shaker K+ channel genes was tissue or developmental stage specific. The transcription levels of Shaker K+ channel genes in foxtail millet under different abiotic stresses (cold, heat, NaCl, and PEG) and phytohormones (6-BA, BR, MJ, IAA, NAA, GA3, SA, and ABA) treatments at 0, 12, and 24 h were detected by qRT-PCR. The results showed that SiAKT1, SiKAT3, SiGORK, and SiSKOR were worth further research due to their significant responses after most treatments. The yeast complementation assay verified the inward K+ transport activities of detectable Shaker K+ channels. Finally, we found interactions between SiKAT2 and SiSNARE proteins. Compared to research in Arabidopsis, our results showed a difference in SYP121 related Shaker K+ channel regulation mechanism in foxtail millet. Our results indicate that Shaker K+ channels play important roles in foxtail millet and provide theoretical support for further exploring the K+ absorption mechanism of foxtail millet under abiotic stress.

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“…Codon bias is the result of non-random mutational patterns, selectional forces, and genome composition. It is related to the gene expression level [ 12 ], gene length [ 13 ], selective transcription [ 14 ], presence of rare codons [ 15 ], preferred codons [ 16 ], preferred codon pairs [ 17 ], protein properties [ 18 ], mRNA structure [ 19 ] roles of translation efficacy [ 20 ] and accuracy [ 21 ]; accordingly, virus fitness in any host [ 22 ] may be explained. Unfit viruses are attenuated in their infectivity and may serve as a vaccine candidate.…”

Section: Introductionmentioning

confidence: 99%

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

et al. 2023

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Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.

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Codon Bias Can Determine Sorting of a Potassium Channel Protein

Cited by 8 publications

References 54 publications

Current Challenges of Mitochondrial Potassium Channel Research

Current Challenges of Mitochondrial Potassium Channel Research

Identification and Characterization of Shaker K+ Channel Gene Family in Foxtail Millet (Setaria italica) and Their Role in Stress Response

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

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