Molecular characterization and expression pattern of Rubisco activase gene GhRCAβ2 in upland cotton (Gossypium hirsutum L.)

Chao Maoni,Huang Ling,Dong Jie,Chen Yu,Hu Genhai,Zhang Qiufang,Zhang Jinbao,Wang Qinglian 한국유전학회 2024 Genes & Genomics Vol.46 No.4

Background Rubisco activase (RCA) is a pivotal enzyme that can catalyse the activation of Rubisco in carbon assimilation pathway. Many studies have shown that RCA may be a potential target for genetic manipulation aimed at enhancing photosynthetic efficiency and crop yield. Objective To understand the biological function of the GhRCAβ2 gene in upland cotton, we cloned the coding sequence (CDS) of the GhRCAβ2 gene and investigated its sequence features, evolutionary relationship, subcellular localization, promoter sequence and expression pattern. Methods The bioinformatics tools were used to analyze the sequence features of GhRCAβ2 protein. Transient transformation of Arabidopsis mesophyll protoplasts was performed to determine the subcellular localization of the GhRCAβ2 protein. The expression pattern of the GhRCAβ2 gene was examined by analyzing transcriptome data and using the quantitative real-time PCR (qRT-PCR). Results The full-length CDS of GhRCAβ2 was 1317 bp, and it encoded a protein with a chloroplast transit peptide. The GhRCAβ2 had two conserved ATP-binding domains, and did not have the C-terminal extension (CTE) domain that was unique to the RCA α-isoform in plants. Evolutionarily, GhRCAβ2 was clustered in Group A, and had a close evolutionary relationship with the soybean RCA. Western blot analysis demonstrated that GhRCAβ2 was immunoreactive to the RCA antibody displaying a molecular weight similar to that of the RCA β-isoform. The GhRCAβ2 protein was found in chloroplast, aligning with its role as a vital enzyme in the process of photosynthesis. The GhRCAβ2 gene had a leaf tissue-specific expression pattern, and the yellow-green leaf mutant exhibited a decreased expression of GhRCAβ2 in comparison to the wild-type cotton plants. The GhRCAβ2 promoter contained several cis-acting elements that respond to light, phytohormones and stress, suggesting that the expression of GhRCAβ2 may be regulated by these factors. An additional examination of stress response indicated that GhRCAβ2 expression was influenced by cold, heat, salt, and drought stress. Notably, diverse expression pattern was observed across different stress conditions. Additionally, low phosphorus and low potassium stress may result in a notable reduction in the expression of GhRCAβ2 gene. Conclusion Our findings will establish a basis for further understanding the function of the GhRCAβ2 gene, as well as providing valuable genetic knowledge to improve cotton photosynthetic efficiency and yield under challenging environmental circumstances. Background Rubisco activase (RCA) is a pivotal enzyme that can catalyse the activation of Rubisco in carbon assimilation pathway. Many studies have shown that RCA may be a potential target for genetic manipulation aimed at enhancing photosynthetic efficiency and crop yield. Objective To understand the biological function of the GhRCAβ2 gene in upland cotton, we cloned the coding sequence (CDS) of the GhRCAβ2 gene and investigated its sequence features, evolutionary relationship, subcellular localization, promoter sequence and expression pattern. Methods The bioinformatics tools were used to analyze the sequence features of GhRCAβ2 protein. Transient transformation of Arabidopsis mesophyll protoplasts was performed to determine the subcellular localization of the GhRCAβ2 protein. The expression pattern of the GhRCAβ2 gene was examined by analyzing transcriptome data and using the quantitative real-time PCR (qRT-PCR). Results The full-length CDS of GhRCAβ2 was 1317 bp, and it encoded a protein with a chloroplast transit peptide. The GhRCAβ2 had two conserved ATP-binding domains, and did not have the C-terminal extension (CTE) domain that was unique to the RCA α-isoform in plants. Evolutionarily, GhRCAβ2 was clustered in Group A, and had a close evolutionary relationship with the soybean RCA. Western blot analysis demonstrated that GhRCAβ2 was immunoreactive to the RCA antibody displaying a molecular weight similar to that of the RCA β-isoform. The GhRCAβ2 protein was found in chloroplast, aligning with its role as a vital enzyme in the process of photosynthesis. The GhRCAβ2 gene had a leaf tissue-specific expression pattern, and the yellow-green leaf mutant exhibited a decreased expression of GhRCAβ2 in comparison to the wild-type cotton plants. The GhRCAβ2 promoter contained several cis-acting elements that respond to light, phytohormones and stress, suggesting that the expression of GhRCAβ2 may be regulated by these factors. An additional examination of stress response indicated that GhRCAβ2 expression was influenced by cold, heat, salt, and drought stress. Notably, diverse expression pattern was observed across different stress conditions. Additionally, low phosphorus and low potassium stress may result in a notable reduction in the expression of GhRCAβ2 gene. Conclusion Our findings will establish a basis for further understanding the function of the GhRCAβ2 gene, as well as providing valuable genetic knowledge to improve cotton photosynthetic efficiency and yield under challenging environmental circumstances.

Nutritional and Tissue Specificity of IGF-I and IGFBP-2 Gene Expression in Growing Chickens - A Review -

Kita, K.,Nagao, K.,Okumura, J. Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.5

Nutritional regulation of gene expression associated with growth and feeding behavior in avian species can become an important technique to improve poultry production according to the supply of nutrients in the diet. Insulin-like growth factor-I (IGF-I) found in chickens has been characterized to be a 70 amino acid polypeptide and plays an important role in growth and metabolism. Although it is been well known that IGF-I is highly associated with embryonic development and post-hatching growth, changes in the distribution of IGF-I gene expression throughout early- to late-embryogenesis have not been studied so far. We revealed that the developmental pattern of IGF-I gene expression during embryogenesis differed among various tissues. No bands of IGF-I mRNA were detected in embryonic liver at 7 days of incubation, and thereafter the amount of hepatic IGF-I mRNA was increased from 14 to 20 days of incubation. In eyes, a peak in IGF-I mRNA levels occurred at mid-embryogenesis, but by contrast, IGF-I mRNA was barely detectable in the heart throughout all incubation periods. In the muscle, no significant difference in IGF-I gene expression was observed during different stages of embryogenesis. After hatching, hepatic IGF-I gene expression as well as plasma IGF-I concentration increases rapidly with age, reaches a peak before sexual maturity, and then declines. The IGF-I gene expression is very sensitive to changes in nutritional conditions. Food-restriction and fasting decreased hepatic IGF-I gene expression and refeeding restored IGF-I gene expression to the level of fed chickens. Dietary protein is also a very strong factor in changing hepatic IGF-I gene expression. Refeeding with dietary protein alone successfully restored hepatic IGF-I gene expression of fasted chickens to the level of fed controls. In most circumstances, IGF-I makes a complex with specific high-affinity IGF-binding proteins (IGFBPs). So far, four different IGFBPs have been identified in avian species and the major IGFBP in chicken plasma has been reported to be IGFBP-2. We studied the relationship between nutritional status and IGFBP-2 gene expression in various tissues of young chickens. In the liver of fed chickens, almost no IGFBP-2 mRNA was detected. However, fasting markedly increased hepatic IGFBP-2 gene expression, and the level was reduced after refeeding. In the gizzard of well-fed young chickens, IGFBP-2 gene expression was detected and fasting significantly elevated gizzard IGFBP-2 mRNA levels to about double that of fed controls. After refeeding, gizzard IGFBP-2 gene expression decreased similar to hepatic IGFBP-2 gene expression. In the brain, IGFBP-2 mRNA was observed in fed chickens and had significantly decreased by fasting. In the kidney, IGFBP-2 gene expression was observed but not influenced by fasting and refeeding. Recently, we have demonstrated in vivo that gizzard and hepatic IGFBP-2 gene expression in fasted chickens was rapidly reduced by intravenous administration of insulin, as indicated that in young chickens the reduction in gizzard and hepatic IGFBP-2 gene expression in vivo stimulated by malnutrition may be, in part, regulated by means of the increase in plasma insulin concentration via an insulin-response element. The influence of dietary protein source (isolated soybean protein vs. casein) and the supplementation of essential amino acids on gizzard IGFBP-2 gene expression was examined. In both soybean protein and casein diet groups, the deficiency of essential amino acids stimulated chickens to increase gizzard IGFBP-2 gene expression. Although amino acid supplementation of a soybean protein diet significantly decreased gizzard IGFBP-2 mRNA levels, a similar reduction was not observed in chickens fed a casein diet supplemented with amino acids. This overview of nutritional regulation of IGF-I and IGFBP-2 gene expression in young chickens would serve for the establishment of the supply of nutrients to diets to improve poultry pro

Gene expression profiling of kidneys from Sprague-Dawley rats following 12-week inhalation exposure to silver nanoparticles

Dong, Mi Sook,Choi, Ji-Yoon,Sung, Jae Hyuck,Kim, Jin Sik,Song, Kyung Seuk,Ryu, Hyun Ryol,Lee, Ji Hyun,Bang, In Seok,An, Kangho,Park, Hyun Min,Song, Nam Woong,Yu, Il Je Informa Healthcare USA, Inc. 2013 Toxicology mechanisms and methods Vol.23 No.6

<P>The specific properties of silver nanoparticles (AgNPs), such as antimicrobial activity and electrical conductivity, allow them to be used in many fields. However, their expanding application is also raising health, environmental and safety concerns. Previous <I>in vivo</I> AgNP toxicity studies have indicated a gender-different accumulation of silver in the kidneys, with 2-3 times more silver in female kidneys compared to male kidneys. However, no other studies have further addressed this gender difference. Accordingly, the current study investigated the gender-dependent effect of AgNPs on the kidney gene level based on toxicogenomic studies of kidneys obtained from rats exposed to AgNPs via inhalation for 12 weeks. When compared with the fresh air control, the silver nanoparticle-exposed kidneys included 104 genes with a more than 1.3-fold expression increase. For the male rat kidneys exposed to a low or high dose of silver nanoparticles, 96 genes exhibited expression changes, where six genes changed with both the low and high dose; four increased and two decreased. Meanwhile, for the female rat kidneys exposed to a low or high dose of silver nanoparticles, 66 genes exhibited expression changes, where 11 genes changed with both the low and high dose; nine increased and two decreased. Gender-dependent gene expression changes of more than 2-fold were linked to 163 genes, with 79 genes in the male kidneys and 84 genes in the female kidneys, plus gender-dependent gene expression changes of more than 5-fold were linked to 21 genes. However, no genes involved in apoptosis or the cell cycle were activated by the 12-week silver nanoparticle inhalation exposure. Overall, the male rat kidneys showed a higher expression of genes involved in xenobiotic metabolism, while the female rat kidneys showed a higher expression of genes involved in extracellular signaling.</P>

Gene Expression of Heart and Adipocyte Fatty Acid-binding Protein in Chickens by FQ-RT-PCR

Tu, Yunjie,Su, Yijun,Wang, Kehua,Zhang, Xueyu,Tong, Haibing,Gao, Yushi Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.8

This study was to detect the expression of heart fatty acid-binding protein (H-FABP) and adipocyte fatty acid-binding protein (A-FABP) gene mRNA in different tissues of Rugao and Luyuan chickens at 56 d and 120 d by real-time fluorescence quantitative reverse transcription polymerase-chain reaction (FQ-RT-PCR). The primers were designed according to the sequences of HFABP, A-FABP and GAPDH genes in Gallus gallus, which were used as target genes and internal reference gene, respectively. The levels of H-FABP and A-FABP gene expression were detected by SYBR Green I FQ-RT-PCR. The relative H-FABP and A-FABP gene mRNA expression level was calculated with 2-$^{{\Delta}Ct}$. Melting curve analysis showed a single peak of three genes. Intramuscular fat (IMF) content in breast muscle and leg muscle of the two chicken breeds at 120 d was higher than at 56 d. IMF content in breast muscle and leg muscle at 56 d and 120 d in Luyuan was significantly higher than in Rugao, however, abdominal fat of Luyuan was significantly lower than that of Rugao. The relative H-FABP gene mRNA expression level in cardiac muscle was the highest in both chicken breeds. The relative H-FABP and A-FABP gene expression of different tissues in Luyuan was higher than in Rugao. H-FABP gene mRNA expression had a negative effect on IMF of leg and breast muscles, and was significantly negatively correlated with IMF content. The relative A-FABP gene mRNA level in abdominal fat was higher than in liver. The A-FABP gene mRNA was not expressed in leg, breast and cardiac muscles. A-FABP gene mRNA expression level was significantly positively correlated with abdominal fat and had a significant effect on abdominal fat but not IMF content.

Analysis of Gene Expression Profiles of Liver Stellate Cells During Liver Regeneration in Rats

Xu Cunshuan,Chen Xiaoguang,Chang Cuifang,Wang Gaiping,Wang Wenbo,Zhang Lianxing,Zhu Qiushi,Wang Lei,Zhang Fuchun 한국분자세포생물학회 2011 Molecules and cells Vol.31 No.1

This study performed a large-scale, high-throughput analy-sis of transcriptional profiling of liver stellate cells (LSCs) at the cellular level to investigate changes in the biological activity of LSCs during rat liver regeneration (LR) and the relation of these changes to LR. First, a rat liver regeneration model was established by partial hepatectomy (PH). Stellate cells were isolated in high purity and yield from the regenerating rat liver by Percoll density gradient centrifugation and immunomagnetic bead sorting. The changes in gene expression of LSCs after PH were examined using a rat genome 230 2.0 array composed of 24622 genes. The results indicated that 10241 of the 24622 genes investigated on the array were differentially expressed in LSCs. Of the 10241 genes, 1563 known genes were related to LR, which were grouped into three major gene expression clusters according to three-fold cut-off threshold: the up-regulated gene cluster, the down-regulated gene cluster, and the cluster composed of genes showing complex changes in expression. Additionally, the genes were grouped into those involved in transcription regulation, signal transduction, transport, cellular metabolism, in-flammation and immunity by functional analysis. When gene expression profiles were combined with the results of gene functional analysis, most of the genes involved in cytokine secretion and retinol metabolism in LSCs were significantly enriched in the cluster characterized by decreased expression, whereas genes involved in lipid metabolism were mostly enriched in the cluster showing increased expression. Based on further analysis of genes expressed in a phase-dependent manner during LR, it was suggested that lipid metabolism in LSCs was enhanced in the whole regeneration process, and that immune response and cytokine secretion were impaired during all three regenerative phases.

Study on the differential gene expression of elm leaves fed on by Tetraneura akinire Sasaki

Hai‑bo Lu,Ling‑pin Jin,Dong Wei,Zhi‑hong Huang 한국유전학회 2019 Genes & Genomics Vol.41 No.12

Background To study the essential molecular mechanism of gall formation is very important. Objective To investigate the differential gene expression in leaves fed on by Tetraneura akinire Sasaki and to provide a basis for the better understanding of the essential molecular mechanism of gall formation. Methods The infected leaves of the elm were divided into three periods: initial formation period (T2), growth and differentiation period (T3), and cracking period (T4). The untouched leaves were used as the control (T1). RNA-Seq was performed, and the high-quality sequences were mapped to the reference genome and the elm gene database to obtain the gene expression profiles. The expression level of each gene was calculated by the RPKM method. A combination of FDR ≤ 0.01 and the absolute value of |log2 ratio (T/CK)| ≥ 2 was used as the threshold to determine the significance of gene expression. Finally, GO and pathway enrichment analyses were used to identify the significantly enriched functional classification and metabolic pathways in DEGs. Results The results revealed that approximately 244 mRNAs were detected between T1 and T2, including 192 up-regulated and 52 down-regulated mRNAs; approximately 175 mRNAs were detected between T1 and T3, including 145 up-regulated and 30 down-regulated mRNAs; and approximately 372 mRNAs were detected between T1 and T4, including 360 up-regulated and 12 down-regulated mRNAs. Approximately 34 differentially expressed genes were identified by Venn analysis. Comparing the three infection periods to the control, there were 28 up-regulated and six down-regulated mRNAs. Additionally, 562 genes were used for cluster analysis, which revealed that the gene expression in T2 and T3 changed greatly. Genes related to cell proliferation and respiration, such as microtubulin and 6-phosphoric acid fructose kinase were mainly up-regulated during the T2 period. Genes encoding lipoxygenase, glutathione-S-transferase, superoxide dismutase and protease inhibitor were up-regulated during T2 and T3. Genes encoding lignocellulose synthase were up-regulated during T4, which suggests the reinforcement of the cell wall to improve the resistance to the damage of the Tetraneura akinire Sasaki. Conclusions The results showed that the feeding of Tetraneura akinire Sasaki caused the differential expression of elm genes and influenced cellular energy metabolism. These changes in physiological response and gene expression of the elm compose the physiological and molecular basis of the gall formation and may improve the resistance of elm to Tetraneura akinire Sasaki.

Expression of the Drosophila p38b Gene Promoter during Development and in the Immune Response

Park, Joung-Sun,Kim, Young-Shin,Park, So-Young,Yoo, Mi-Ae 한국유전학회 2003 Genes & Genomics Vol.25 No.3

p38 MAPK have been extensively studied as a stress-responsive kinase and recently its role during development was reported. However, the mechanisms by which p38 gene expression is regulated remains unknown. In this study, to investigate expression of the Drosophila p38b (D-p38b) gene, we established transgenic flies bearing the D-p38b-lacZ fusion genes containing the D-p38b promoter region (-901 to +208 with respect to the transcription initiation site). Levels of the D-p38b mRNA examined by RT-PCR and analyses of expression patterns of the D-p38b-lacZ in transgenic flies indicated that the D-p38b gene is expressed throughout development. Expression of the D-p38b-lacZ gene during embryogenesis was similar to that of the D-p38b gene in situ reported by other group. The results indicated that the promoter region is sufficient for endogenous expression of the D-p38b gene. Strong expression of the D-p38b-lacZ gene was detected in the brain and ganglion, imaginal disc, salivary gland, gut and fat body among larval tissues and in the gut, fat body and reproductive systems of adult female and male. Interestingly, upregulated expression of the D-p38b-lacZ gene in the fat body and gut by injury was detected. Transgenic flies bearing the D-p38b-lacZ fusion gene promise to be useful for further studies on the mechanisms of regulation of the D-p38b gene expression during development and in the immune response.

랜드마크 유전자 기반 목표 유전자 발현량 예측을 위한 특징 추출 심층 신경망

이다빈,황규백 한국정보과학회 2020 정보과학회 컴퓨팅의 실제 논문지 Vol.26 No.8

Gene expression profiling is useful for disease studies. Researchers of the Library of Integrated Network-Based Cellular Signatures Program developed an efficient profiling method in which the expression level of only a subset of the human genes (landmark genes), comprising approximately 80% of the entire gene expression information, is measured, and subsequently used for predicting the expression level of the other genes (target genes). In this study, we propose a method to extract non-linear features of the landmark genes using autoencoders and then predict the expression level of the target genes using the extracted features. In the experiments on 111,009 gene-expression profiles, comprising 943 landmark genes and 9,520 target genes, our method reduced the prediction error for approximately 95% of the target genes compared with a previous deep neural network model. The average proportion of error reduction was approximately 7%. This result suggests that the non-linear feature extraction can improve the accuracy of target-gene expression prediction from the landmark genes. 유전자 발현 프로파일링은 질병 연구에 유용하다. Library of Integrated Network-Based Cellular Signatures 프로그램 연구진은 전체 인간 유전자 발현 정보의 약 80%를 포함하는 소수의 유전자(랜드마크 유전자) 발현량만을 측정한 뒤 다른 유전자(목표 유전자)의 발현량을 예측하는 효율적인 프로파일링 기법을 개발했다. 본 논문에서는 오토인코더로 랜드마크 유전자의 비선형 특징을 추출한 후 이에 기반하여 목표 유전자의 발현량을 예측하는 방법을 제안한다. 이 방법은 943개의 랜드마크 유전자와 9,520개의 목표 유전자로 구성된 111,009개의 유전자 발현 프로파일에 대한 실험에서 기존의 심층 신경망과 비교했을 때 약 95%의 목표 유전자에 대해 예측 오류를 감소시켰으며, 감소의 폭은 평균적으로 약 7%였다. 이러한 결과는 오토인코더 기반의 비선형 특징 추출이 랜드마크 유전자로부터 목표 유전자의 발현량을 예측하는 데 기여할 수 있음을 시사한다.

Expression of Coat Color Associated Genes in Korean Brindle Cattle by Microarray Analysis

Hae-Lee Lee,Jae-Hee Park,Jong Gug Kim 한국수정란이식학회 2015 한국동물생명공학회지 Vol.30 No.2

The aim of the present study was to identify coat color associated genes that are differentially expressed in mature Korean brindle cattle (KBC) with different coat colors and in Hanwoo cows. KBC calves, before and after coat color appearance, were included. Total cellular RNA was isolated from the tail hair cells and used for microarray. The number of expressed coat color associated genes/probes was 5813 in mature KBC and Hanwoo cows. Among the expressed coat color associated genes/probes, 167 genes were the coat color associated genes listed in the Gene card database and 125 genes were the pigment and melanocyte genes listed in the Gene ontology_bovine database. There were 23 genes/probes commonly listed in both databases and their expressions were further studied. Out of the 23 genes/probes, MLPH, PMEL, TYR and TYRP1 genes were expressed at least two fold higher (p<0.01) levels in KBC with brindle color than either Hanwoo or KBC with brown color. TYRP1 expression was 22.96 or 19.89 fold higher (p<0.01) in KBC with brindle color than either Hanwoo or KBC with brown color, respectively, which was the biggest fold difference. The hierarchical clustering analysis indicated that MLPH, PMEL, TYR and TYRP1 were the highly expressed genes in mature cattle. There were only a few genes differentially expressed after coat color appearance in KBC calves. Studies on the regulation and mechanism of gene expression of highly expressed genes would be next steps to better understand coat color determination and to improve brindle coat color appearance in KBC.

Enhancing performance of gene expression value prediction with cluster-based regression

석호식 한국유전학회 2021 Genes & Genomics Vol.43 No.9

Background The inherent correlations among gene expressions have received attention. Recently, it was reported that a set of approximately 1000 landmark genes can be utilized for prediction of expression of other genes (target genes). Objective The objective of this study is to predict expression values of target genes based on expression values of landmark genes. Methods A cluster-based regression method is proposed. In the proposed method, clusters are obtained from a set of training instances of a gene and an estimator is obtained per cluster. A test instance is assigned to one of clusters then a regression model corresponding to the cluster predicts expression value. Results Performance of the proposed method is measured on the GEO (Gene Expression Omnibus) expression data and the GTEx (Genotype-Tissue Expression) expression data. In terms of mean absolute error averaged across target genes, the proposed method signifcantly outperforms previous approaches in the case of the GEO expression data. Conclusions The experimental results report that the combination of clustering and regression can outperform the state-ofthe art methods such as generative adversarial networks and a gradient boosting based method.