Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole<i> Mycobacterium tuberculosis</i> Coding Genome from Different Area

Li, Gun; Ren, Yi; Haixian, Pan; Zhang, Liang

doi:10.1155/2018/3574976

Cited by 34 publications

(27 citation statements)

References 36 publications

(37 reference statements)

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“…463 CAI is often correlated with GC3% yet this correlation was only significant when concerning 464 ASR genes and not the LP3 genes. Instead CAI was positively correlated with GC1% in LP3, 465 which contrasts with previous gene studies (Gun et al, 2018;Song et al, 2017Song et al, , 2018. Our 466 study does reflect significant correlations between CAI and ENC within the ABA/WDS genes, 467 indicative of a high translation efficiency found in many highly expressed genes (Sharp and Li, 468 1987;Wright, 1990) 469…”

Section: Previous Gene Studies Have Focused On the Correlations Of Cacontrasting

confidence: 68%

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Evolutionary analysis of LP3 gene family in conifers: an ASR homolog

García‐Gil

Lecoy

2020

Preprint

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8Drought has long been established as a major environmental stress for plants which have in turn 9 developed several coping strategies, ranging from physiological to molecular mechanisms. 10 LP3; a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene was first detected in 11 tomato; and has been shown to be present in four different isoforms in loblolly pine called LP3-12 0, LP3-1, LP3-2 and LP3-3. While ASR has already been extensively studied notably in tomato, 13 the same cannot be said of LP3. Like ASR, the different LP3 isoforms have been shown to be 14 upregulated in response to water deficit stress and to also act as transcription factors for genes 15 likely involved in hexose transport. In this study we have investigated the evolutionary history 16 of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective 17 and comparing the differences in selective pressure and codon usage. Phylogenetic analyses of 18 different LP3 homologs compared to ASR show that LP3 is less divergent across species than 19 ASR and that even when comparing the different sub-sections of the gene the divergence rate 20 of LP3 is lower than that of ASR. Analysis of different gene parameters showed that there were 21 differences in GC1% and GC2% but not in total or GC3% content. All genes had a relatively 22 high CAI value associated with a low to moderate ENC value, which is indicative of high 23 translation efficiency found in highly expressed genes. Analysis of codon usage also showed 24 that LP3 preferentially uses different codons than ASR. Selective pressure analysis across most 25 of the LP3 and ASR genes used in this study showed that these genes were principally 26 undergoing purifying selection, with the exception of LP3-3 which seems to be undergoing 27 diversifying selection most probably due to the fact that it likely recently diverged from LP3-28 0. This study thus provides insight in how ASR and LP3 have diverged from each other while 29 remaining homologous. 30

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Section: Previous Gene Studies Have Focused On the Correlations Of Cacontrasting

confidence: 68%

“…as gene length, GC content and ENC (Gun et al, 2018;Song et al, 2017Song et al, , 2018Zhou and Li, 462 2009). Our study however showed no significant correlation between sequence length and CAI.…”

Section: Previous Gene Studies Have Focused On the Correlations Of Camentioning

confidence: 99%

Evolutionary analysis of LP3 gene family in conifers: an ASR homolog

García‐Gil

Lecoy

2020

Preprint

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“…emrB ( Rv0783c ) belongs to the major facilitator superfamily (MFS) characteristically energized by the proton motive force (H + or Na + ) 50,51 , and may confer low-level resistance to RMP 52 . Although the role of I461I in emrB in KwaZulu-Natal’s population is unknown at present, this synonymous mutation (c.1383 C > A, ATC > ATA) is very rare in terms of codon usage of Mtb 53 , and the significance of codon usage bias and t-RNA modification should be taken into account, because rare codons are sometimes advantageous to the survival of Mtb under stress conditions 54 . When exposed to INH, various MFS efflux pump genes were reported to be overexpressed 50 , and these may induce sustained increased efflux activity with selection and stabilization of drug-resistant mutations 55 .…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam

Hang

Hijikata

Maeda

et al. 2019

Sci Rep

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Drug-resistant tuberculosis (TB) is a serious global problem, and pathogen factors involved in the transmission of isoniazid (INH)-resistant TB have not been fully investigated. We performed whole genome sequencing of 332 clinical Mycobacterium tuberculosis (Mtb) isolates collected from patients newly diagnosed with smear-positive pulmonary TB in Hanoi, Vietnam. Using a bacterial genome-wide approach based on linear mixed models, we investigated the associations between 31-bp k-mers and clustered strains harboring katG-S315T, a major INH-resistance mutation in the present cohort and in the second panel previously published in South Africa. Five statistically significant genes, namely, PPE18/19, gid, emrB, Rv1588c, and pncA, were shared by the two panels. We further identified variants of the genes responsible for these k-mers, which are relevant to the spread of INH-resistant strains. Phylogenetic convergence test showed that variants relevant to PPE46/47-like chimeric genes were significantly associated with the same phenotype in Hanoi. The associations were further confirmed after adjustment for the confounders. These findings suggest that genomic variations of the pathogen facilitate the expansion of INH-resistance TB, at least in part, and our study provides a new insight into the mechanisms by which drug-resistant Mtb maintains fitness and spreads in Asia and Africa.

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“…Nilai CAI merupakan salah satu parameter yang digunakan untuk memprediksi tingkat ekspresi gen yang nilainya berkisar dari nol hingga satu (Gun et al, 2018). Nilai CAI Lon-like IIA-1A5 setelah dioptimasi adalah 0,97, nilai ini dikategorikan baik karena menunjukkan tingkat ekspresi gen yang tinggi.…”

Section: Optimasi Gen Penyandi Lon-like Proteaseunclassified

“…Kisaran nilai CAI yang baik adalah > 0,8 -1,0 (GenScript, 2019). Semakin besar nilainya, maka semakin kuat bias penggunaan kodon, bernilai satu jika gen selalu digunakan untuk sintesis setiap asam amino yang dikodekan (Gun et al, 2018). Persentase kandungan GC dari gen hasil optimasi meningkat menjadi 56,57% dan berada dalam kisaran persentase ideal yaitu 30-70% (GenScript, 2019).…”

Section: Optimasi Gen Penyandi Lon-like Proteaseunclassified

Expression of Lon-like Protease Gene from Lactobacillus plantarum IIA-1A5 in Escherichia coli BL21(DE3)

et al. 2019

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Proteases are one of most important and abundant enzymes produced by the biotechnology industry, for scientific, physiological and industrial application and dominates of the whole enzyme market. Lactobacillus plantarum IIA-1A5 is an Indonesian lactic acid bacteria (LAB) isolated from beef Peranakan Ongole cattle. Preliminary analysis on its whole genome sequence indicated that this strain harbours some genes involved in protein degradation and might be promising to be further applied. This study aims to optimize the gene sequence of a lon-like protease of L. plantarum IIA-1A5 for heterologous expression system. The Lon-like gene expression system is made using genes that have been optimized first in silico. pET-28a(+), E. coli BL21(DE3), Nde1 and BamH1 were used in this study as a expression vector, a host and retriction enzyme, respectively. Molecular weight was validated using SDS-PAGE and expasy.org software. The results showed that optimization increased codon adaptation index value (CAI) and GC content to 0.97 and 56.57%, respectively, which were suitable for the E. coli expression system. The Lon-like IIA gene was successfully expressed in the cell cytoplasm by induction of 1 mM Isopropyl β-D-1-thiogalactopyranoside (IPTG) at 37 °C. As many as 88% of Lon-like IIA codons were distributed in the 91-100 quality group. Lon-like IIA was successfully expressed in a host cell induced with 1 mM IPTG at 37oC . IPTG induction was performed at the 3rd hour of incubation with OD600 0.59. In addition, Lon-like IIA molecular weight was detected approximately 43 kDa.

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Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Cited by 34 publications

References 36 publications

Evolutionary analysis of LP3 gene family in conifers: an ASR homolog

Evolutionary analysis of LP3 gene family in conifers: an ASR homolog

Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam

Expression of Lon-like Protease Gene from Lactobacillus plantarum IIA-1A5 in Escherichia coli BL21(DE3)

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