• Journal of Microbiology and Biotechnology
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• v.16 no.4
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• pp.623-632
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• 2006

To find potential targets of novel antimicrobial agents, we identified essential genes of Staphylococcus aureus N315 by using comparative genomics and allele replacement mutagenesis. By comparing the genome of S. aureus N315 with those of Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Streptococcus pneumoniae, a total of 481 candidate target genes with similar amino acid sequences with at least three other species by >40% sequence identity were selected. of 481 disrupted candidate genes, 122 genes were identified as essential genes for growth of S. aureus N315. Of these, 51 essential genes were those not identified in any bacterial species, and 24 genes encode proteins of unknown function. Seventeen genes were determined as non-essential although they were identified as essential genes in other strain of S. aureus and other species. We found no significant difference among essential genes between Streptococcus pneumoniae and S. aureus with regard to cellular function.

• Molecules and Cells
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• v.19 no.3
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• pp.365-374
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• 2005

To find potential targets of novel antimicrobial agents, we identified essential genes of Streptococcus pneumoniae using comparative genomics and allelic replacement mutagenesis. We compared the genome of S. pneumoniae R6 with those of Bacillus subtilis, Enterococcus faecalis, Escherichia coli, and Staphylococcus aureus, and selected 693 candidate target genes with > 40% amino acid sequence identity to the corresponding genes in at least two of the other species. The 693 genes were disrupted and 133 were found to be essential for growth. Of these, 32 encoded proteins of unknown function, and we were able to identify orthologues of 22 of these genes by genomic comparisons. The experimental method used in this study is easy to perform, rapid and efficient for identifying essential genes of bacterial pathogens.

• Biomolecules & Therapeutics
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• v.29 no.2
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• pp.234-247
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• 2021

We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the Erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.

• Molecules and Cells
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• v.19 no.3
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• pp.452-457
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• 2005

The adaptor protein (AP) complexes are involved in membrane transport of many proteins. There are 3 AP complexes in C. elegans unlike mammals that have four. To study the biological functions of the AP-3 complexes of C. elegans, we sought homologues of the mouse and human genes that encode subunits of the AP-3 complexes by screening C. elegans genomic and EST sequences. We identified single copies of homologues of the ${\mu}3$, ${\sigma}3$, ${\beta}3$ and ${\delta}$ genes. The medium chain of AP-3 is encoded by a single gene in C. elegans but two different genes in mammals. Since there are no known mutations in these genes in C. elegans, we performed RNAi to assess their functions in development. RNAi of each of the genes caused embryonic and larval lethal phenotypes. APM-3 is expressed in most cells, particularly strongly in spermatheca and vulva. We conclude that the products of the C. elegans ${\mu}3$, ${\sigma}3$, ${\beta}3$ and d genes are essential for embryogenesis and larval development.

• Animal cells and systems
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• v.5 no.4
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• pp.341-346
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• 2001

Hypertension is a complex disease with strong genetic influences. Essential hypertension has been shown to be associated with insulin resistance. To clarify the genetic basis of insulin resistance in Hypertension, case-control association studies were performed to examine candidate genes for insulin resistance in hypertension. Polymorphisms investigated were the BstO I polymorphism of the $\beta$3-adrenergic receptor (ADRB3) gene, the Xba I Polymorphism of the glycogen synthase (GSY) gene, the Dde I polymorphism of the protein phosphatase 1 G subuit (PP1G) gene, the BstE II polymorphism of the glucagon receptor (GCG-R) gene, the Pst 1 polymorphism of the insulin (INS) gene and the Acc I polymorphism of the glucokinase (GCK) gene. No significant differences were observed in the distribution of alleles and genotypes of the ADRB3, GSY PP1G, GCG-R, INS, and GCK genes between hypertensive and normotensive groups. Although the frequencies in each of these polymorphisms were not significantly different between essential hypertensive and normotensive individuals, our results may provide additional information for linkage analysis and associative studies of disorders in carbohydrate metabolism or in cardiovascular disease.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.11.1-11.8
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• 2012

Genes that are indispensable for survival are referred to as essential gene. Due to the momentous significance of these genes for cellular activity they can be selected potentially as drug targets. Here in this study, an essential gene for Streptococcus suis was predicted using coherent statistical analysis and powerful genome comparison computational method. At first the whole genome protein scatter plot was generated and subsequently, on the basis of statistical significance, a reference genome was chosen. The parameters set forth for selecting the reference genome was that the genome of the query (Streptococcus suis) and subject must fall in the same genus and yet they must vary to a good degree. Streptococcus pneumoniae was found to be suitable as the reference genome. A whole genome comparison was performed for the reference (Streptococcus pneumoniae) and the query genome (Streptococcus suis) and 14 conserved proteins from them were subjected to a screen for potential essential gene property. Among those 14 only one essential gene was found to be with impressive similarity score between reference and query. The essential gene encodes for a type of 'Clp protease'. Clp proteases play major roles in degrading misfolded proteins. Results found here should help formulating a drug against Strptococcus suis which is responsible for mild to severe clinical conditions in human. However, like many other computational studies, the study has to be validated furthermore through in vitro assays for concrete proof.

• Biomedical Science Letters
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• v.18 no.2
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• pp.169-174
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• 2012

The placenta is an extraembryonic tissue that is formed between mother and fetus and mediates delivery of nutrients and oxygen from the mother to the fetus. Because of its essential role in sustaining the growth of the fetus during gestation, defects in its development and function frequently result in fetal growth retardation or intrauterine death, depending on its severity. Vertebrate Hox genes are well known transcription factors that are essential for the proper organization of the body plan during embryogenesis. However, certain Hox genes have been known to be expressed in placenta, implying that Hox genes not only play a crucial role during embryonic patterning but also play an important role in placental development. So far, there has been no report that shows the expression pattern of the whole Hox genes during placentation. In this study, therefore, we investigated the Hox gene expression pattern in mouse placenta, from day 10.5 to 18.5 of gestation using real-time RT-PCR method. In general, the 5' posterior Hox genes were expressed more in the developing placenta compared to the 3' Hox genes. Statistical analysis revealed that the expression of 15 Hox genes (Hoxa9, -a11, -a13/ -b8, -b9/ -c6, -c9, -c13/ -d1, -d3, -d8, -d9, -d10, -d11, -d12) were significantly changed in the course of gestation. The majority of these genes showed highest expression at gestational day 10.5, suggesting their possible role in the early stage during placental development.

• Animal Bioscience
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• v.37 no.8
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• pp.1483-1494
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• 2024

Objective: This study was conducted to investigate the effect of slaughter age on carcass traits, meat quality, and the relative mRNA levels of lipid metabolism-related genes in different muscles of Taihang black goats. Methods: In this study, the triceps brachii (TB), longissimus dorsi (LD) and gluteus (GL) muscles of 15 grazing Taihang black goats slaughtered at the age of 2, 3, and 4 (designated as 2-year-old, 3-year-old, and 4-year-old, respectively) were collected. The differences in carcass shape, meat quality, amino acid composition and lipid metabolism gene expression among Taihang black goats of different ages and from different plant parts were compared. Results: Compared with goats at other ages, goats slaughtered at the age of 4 had greater live and carcass weights, meat weights, bone weights and skin areas (p<0.05). LD in the 4-years-old had the lowest cooking loss and moisture content. The crude protein content in the LD of 2-year-old was significantly greater than that in the other age group, and at the age of 2, the LD had the highest crude protein content than TB and GL. The highest fat content was in LD, followed by TB, for goats slaughtered at the age of 4. Eight out of 9 essential amino acids had higher content in the TB compared with other muscles, regardless of age. The total essential amino acid content was highest in the 4-year-old and lowest in the GL muscle at the age of 3. The sterol regulatory element-binding protein-1c (SREBP-1c) and adipose triglyceride lipase (ATGL) genes were significantly more abundant in the TB muscle than in the other muscles for goats slaughtered at the age of 2. At the age of 4, the ATGL and peroxisome proliferator-activated receptor γ (PPARγ) genes were significantly more abundant in the GL than in the LD, while the fatty acid synthase (FAS) genes were significantly less abundant in the GL than in the other muscles. Similarly, compared with those in goats of other ages, the relative mRNA expression levels of the FAS and heart-type fatty acid binding protein (H-FABP) genes in goats slaughtered at the age of 4 were the highest, and the relative mRNA expression of the PPARγ gene was the lowest (p<0.05). The relative mRNA expression of the H-FABP and FAS genes was positively correlated with the intramuscular fat (IMF) content, while the relative mRNA expression levels of the PPARγ and ATGL genes was negatively correlated with the IMF content. Conclusion: Overall, a better nutritional value was obtained for TB from 4-year-old goats, in which the total essential amino acid and fat contents were greater than those of other muscles. The comprehensive action of lipid metabolism genes was consistent with that of the IMF content, among which the FAS, H-FABP, PPARγ, and ATGL genes had positive and negative effects on the process of IMF deposition in Taihang black goats.

• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.57-68
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• 2023

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

• BMB Reports
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• v.46 no.1
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• pp.41-46
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• 2013

Identifying genes indispensable for an organism's life and their characteristics is one of the central questions in current biological research, and hence it would be helpful to develop computational approaches towards the prediction of essential genes. The performance of a predictor is usually measured by the area under the receiver operating characteristic curve (AUC). We propose a novel method by implementing genetic algorithms to maximize the partial AUC that is restricted to a specific interval of lower false positive rate (FPR), the region relevant to follow-up experimental validation. Our predictor uses various features based on sequence information, protein-protein interaction network topology, and gene expression profiles. A feature selection wrapper was developed to alleviate the over-fitting problem and to weigh each feature's relevance to prediction. We evaluated our method using the proteome of budding yeast. Our implementation of genetic algorithms maximizing the partial AUC below 0.05 or 0.10 of FPR outperformed other popular classification methods.