scholarly journals Genome-Wide Analysis and Hormone Regulation of Chitin Deacetylases in Silkworm

2019 ◽  
Vol 20 (7) ◽  
pp. 1679 ◽  
Author(s):  
Ziyu Zhang ◽  
Jiamin Yan ◽  
Qing Liu ◽  
Yuhao Zhang ◽  
Jing Gong ◽  
...  

Chitin deacetylases (CDAs) are a group of enzymes involved in chitin metabolism in insects; they play a critical role in molting, pupation, and the modification of chitin. In this study, we identified several CDAs in the silkworm, Bombyx mori (BmCDA), and investigated the effect of various hormones on their expression in B. mori larvae and embryo cell lines (BmE). Eight genes encoding BmCDAs were identified in the silkworm genome. They showed different expression patterns in different tissues, and were classified into three types based on where they were expressed: the exoskeleton, digestive organs, and genital organs. Moreover, we found that some BmCDAs showed upregulated expression during the molting period, especially during the fourth molting period in larvae. We also verified that the expression of BmCDA1–6 was upregulated by treatment with 20-hydroxyecdysone not only in larvae, but also in BmE cells. Interestingly, juvenile hormone analog treatment also upregulated the expression of some BmCDAs. The overexpression of several transcription factors revealed that the POU transcription factor POUM2 may play a major role in the regulation of BmCDA expression. Finally, the silencing of BmCDA1 and BmCDA2 did not lead to abnormal phenotypes or death, but may have led to delays in silkworm pupation. These results provide important information about lepidopteran insects in terms of chitin deacetylases and the regulation of their expression.

2001 ◽  
Vol 183 (24) ◽  
pp. 7329-7340 ◽  
Author(s):  
Robert Caldwell ◽  
Ron Sapolsky ◽  
Walter Weyler ◽  
Randal R. Maile ◽  
Stuart C. Causey ◽  
...  

ABSTRACT The availability of the complete sequence of the Bacillus subtilis chromosome (F. Kunst et al., Nature 390:249–256, 1997) makes possible the construction of genome-wide DNA arrays and the study of this organism on a global scale. Because we have a long-standing interest in the effects of scoC on late-stage developmental phenomena as they relate toaprE expression, we studied the genome-wide effects of ascoC null mutant with the goal of furthering the understanding of the role of scoC in growth and developmental processes. In the present work we compared the expression patterns of isogenic B. subtilis strains, one of which carries a null mutation in the scoC locus (scoC4). The results obtained indicate thatscoC regulates, either directly or indirectly, the expression of at least 560 genes in the B. subtilisgenome. ScoC appeared to repress as well as activate gene expression. Changes in expression were observed in genes encoding transport and binding proteins, those involved in amino acid, carbohydrate, and nucleotide and/or nucleoside metabolism, and those associated with motility, sporulation, and adaptation to atypical conditions. Changes in gene expression were also observed for transcriptional regulators, along with sigma factors, regulatory phosphatases and kinases, and members of sensor regulator systems. In this report, we discuss some of the phenotypes associated with the scoCmutant in light of the transcriptome changes observed.


2020 ◽  
Author(s):  
Yong Tao ◽  
Shaowen Lu ◽  
Yi Wang ◽  
Cuicui Wei ◽  
Hong Jin ◽  
...  

Abstract Background n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. Results In this study, 0.5% lactate was supplemented into the fermentation with Ruminococcaceae bacterium CPB6 for CA production. Compared to the control (without lactate supplementation), lactate supplementation led to earlier CA production and higher final CA titer and productivity. Transcriptional analysis was carried out using RNA-Seq for the culture with and without lactate supplementation (two groups) at growth and stationary phases, respectively. It has been indicated that 295 genes whose changes in expression patterns were substrate and/or growth dependent. These genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP) and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. Conclusions This study suggested that lactate supplementation can promote CA production by altering the expression patterns of genes involved in the essential metabolic pathways, such as central pyruvate metabolism, the reverse β-oxidation pathway, ABC and PTS transports. The findings presented herein reveal unique insights into the biomolecular effects of lactate on CA production at the gene transcriptional level.


2017 ◽  
Vol 19 (4) ◽  
pp. 627-635 ◽  
Author(s):  
Lijun Lei ◽  
Siyu Xia ◽  
Dan Liu ◽  
Xiaoqing Li ◽  
Jing Feng ◽  
...  

Abstract Long noncoding RNAs (lncRNAs) are a large family of noncoding RNAs that play a critical role in various normal bioprocesses as well as tumorigenesis. However, the expression patterns and biological functions of lncRNAs in acute leukemia have not been well studied. Here, we performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) patient samples, along with non-leukemia control hematopoietic samples. We found that lncRNAs were differentially expressed in AML samples relative to control samples. Notably, we identified that lncRNAs upregulated in AML (relative to the control samples) are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2 and ELK-1 compared with those downregulated in AML. Moreover, an enrichment of H3K4me3 and a depletion of H3K27me3 were observed in upregulated lncRNAs in AML. Expression patterns of three types of lncRNAs (antisense, enhancer and intergenic lncRNAs) have previously been characterized. Of the identified lncRNAs, we found that high expression level lncRNA LOC285758 is associated with the poor prognosis in AML patients. Furthermore, we found that LOC285758 regulates proliferation of AML cell lines by enhancing the expression of HDAC2, a key factor in carcinogenesis. Collectively, our study depicts a landscape of important lncRNAs in AML and provides novel potential therapeutic targets and prognostic markers for AML treatment.


2021 ◽  
Vol 12 ◽  
Author(s):  
Natalia Petrova ◽  
Alsu Nazipova ◽  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Olga Patova ◽  
...  

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.


Author(s):  
Ana López-Varea ◽  
Patricia Vega-Cuesta ◽  
Ana Ruiz-Gómez ◽  
Cristina M Ostalé ◽  
Cristina Molnar ◽  
...  

Abstract The Drosophila genome contains approximately 14.000 protein coding genes encoding all the necessary information to sustain cellular physiology, tissue organization, organism development and behavior. In this manuscript we describe in some detail the phenotypes in the adult fly wing generated after knockdown of approximately 80% of Drosophila genes. We combined this phenotypic description with a comprehensive molecular classification of the Drosophila proteins into classes that summarize the main expected or known biochemical/functional aspect of each protein. This information, combined with mRNA expression levels and in situ expression patterns, provides a simplified atlas of the Drosophila genome, from housekeeping proteins to the components of the signaling pathways directing wing development, that might help to further understand the contribution of each gene group to wing formation.


Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 46 ◽  
Author(s):  
Feng Yan ◽  
Huaizhu Li ◽  
Peng Zhao

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.


2020 ◽  
Author(s):  
YONG TAO ◽  
Shaowen Lu ◽  
Yi Wang ◽  
Cuicui Wei

Abstract Background: n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Our recent studies have demonstrated that lactate can be an attractive energy substrate for the production of CA. However, little is known about the potential molecular mechanism for CA production triggered by the supplementation of exogenous lactate at the gene transcriptional level. Results: 5% lactate was supplemented into the fermentation with Ruminococcaceae bacterium CPB6 for CA production. Results showed that lactate supplementation led to earlier CA production and higher final CA titer and productivity. Transcriptional analysis was carried out using RNA-Seq for the culture with lactate supplementation compared to the control (without lactate supplementation). It has been indicated that there were only 34 differentially expressed genes (DEGs) between the two groups at the exponential phase, of which 15 were upregulated, and 19 were downregulated by more than two-fold. A total of 245 DEGs were identified between the two groups at the stationary phase, of which 123 were upregulated and 122 were downregulated. These DEGs cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP) and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. Conclusion: This study suggested that lactate supplementation can promote CA production by altering the expression patterns of genes involved in the essential metabolic pathways, such as central pyruvate metabolism, the reverse β-oxidation pathway, ABC and PTS transports. The findings presented herein reveal unique insights into the biomolecular effects of lactate on CA production at the gene transcriptional level.


2021 ◽  
Vol 23 (1) ◽  
pp. 196
Author(s):  
Yutong Han ◽  
Ya Yang ◽  
Yan Li ◽  
Xin Yin ◽  
Zhiyu Chen ◽  
...  

The triterpenes in bitter gourd (Momordica charantia) show a variety of medicinal activities. Oxidosqualene cyclase (OSC) plays an indispensable role in the formation of triterpene skeletons during triterpene biosynthesis. In this study, we identified nine genes encoding OSCs from bitter gourd (McOSC1–9). Analyses of their expression patterns in different tissues suggested that characteristic triterpenoids may be biosynthesized in different tissues and then transported. We constructed a hairy root system in which McOSC7 overexpression led to an increased accumulation of camaldulenic acid, enoxolone, and quinovic acid. Thus, the overexpression of McOSC7 increased the active components content in bitter gourd. Our data provide an important foundation for understanding the roles of McOSCs in triterpenoid synthesis.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yanlei Zhai ◽  
Yuanyuan Cui ◽  
Miaoyu Song ◽  
Alexander Vainstein ◽  
Shangwu Chen ◽  
...  

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1–10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207–505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.


2020 ◽  
Author(s):  
Huilin Xiao ◽  
Chaoping Wang ◽  
Nadeem Khan ◽  
Mengxia Chen ◽  
Weihong Fu ◽  
...  

Abstract Background : The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date. Results : We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine. Conclusions : In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.


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