Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents

Chakraborty, Supriyo; Uddin, Arif; Mazumder, Tarikul Huda; Choudhury, Monisha Nath; Malakar, Arup Kumar; Pavlidis, Paul; Halder, Binata; Deka, Himangshu; Mazumder, Gulshana A.; Barbhuiya, Riazul Ahmed; Barbhuiya, Masuk Ahmed; Devi, Warepam Jesmi

doi:10.1016/j.mito.2017.11.006

Cited by 8 publications

(3 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The results thus obtained indicated that both primary forces of nature, mutation pressure and natural selection, shaped the CUB of genes involved in human autophagy. Similar works performed on human mitochondrial genes supported our results, revealing both the key forces of evolution governed the patterns of the CUB in those genes as well [ 60 ]. Moreover, it has been strongly suggested that the CUB of autophagy-related gene ATG13 across different species exhibited a disproportionate influence of mutational pressure and natural selection in its evolution [ 24 ].…”

Section: Discussionsupporting

confidence: 89%

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Jamil

Uddin²,

Alam

et al. 2022

Cells

View full text Add to dashboard Cite

Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.

show abstract

Section: Discussionsupporting

confidence: 89%

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Jamil

Uddin²,

Alam

et al. 2022

Cells

View full text Add to dashboard Cite

show abstract

“…Additionally, Tachinids have to thrive as endo-parasites in highly dioxic environments by adopting a unique respiration strategy 2 , 42 . We postulate that Tachinidae flies have naturally selected for limited GC content and purifying selection to preserve mitochondrial functions, as well as mutational pressure towards biased AT content to reduce the number of effective codons, resulting in a higher rate of energy synthesis at a lower cost 212 , 245 , 250 – 252 . This, in turn, provides a selective energetic advantage to the Tachinids in surviving the hostile environment of the host 253 .…”

Section: Resultsmentioning

confidence: 99%

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Kabiraj

Chetia

Nath

et al. 2022

Sci Rep

View full text Add to dashboard Cite

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

show abstract

“…The human mitochondrial genome contains only 37 genes, of which two are ribosomal RNAs (rRNAs), 22 tRNAs and 13 protein-coding genes. Mammalian mitochondrial DNA (mtDNA) has neither introns nor protective histones, has a high AT content and as a consequence of the small genome size, employs only a small number of tRNAs which are responsible for decoding a large number of codons (21), suggesting that mitochondria show a different codon usage preference from the nuclear genome (21,23). We performed a comparison of codon usage bias and demonstrated that the key rare codon rate in SARS-CoV-2 and S protein were highly similar to the rate seen in mitochondrial genes, and these rates were much higher than found in the human nuclear genome (Fig.…”

Section: Main Textmentioning

confidence: 99%

A novel viral protein translation mechanism reveals mitochondria as a target for antiviral drug development

Cheng

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

The ongoing Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic has acutely highlighted the need to identify new treatment strategies for viral infections. Here we present a pivotal molecular mechanism of viral protein translation that relies on the mitochondrial translation machinery. We found that rare codons such as Leu-TTA are highly enriched in many viruses, including SARS-CoV-2, and these codons are essential for the regulation of viral protein expression. SARS-CoV-2 controls the translation of its spike gene by hijacking host mitochondria through 5' leader and 3'UTR sequences that contain mitochondrial localization signals and activate the EGR1 pathway. Mitochondrial-targeted drugs such as lonidamine and polydatin significantly repress rare codon-driven gene expression and viral replication. This study identifies an unreported viral protein translation mechanism and opens up a novel avenue for developing antiviral drugs.

show abstract

Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents

Cited by 8 publications

References 57 publications

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

A novel viral protein translation mechanism reveals mitochondria as a target for antiviral drug development

Contact Info

Product

Resources

About