Genome-wide Analysis of the Distribution of Riboswitches and Function Analyses of the Corresponding Downstream Genes in Prokaryotes

2018 ◽  
Vol 14 (1) ◽  
pp. 53-61
Author(s):  
Xinfeng Li ◽  
Fang Chen ◽  
Jinfeng Xiao ◽  
Shan-Ho Chou ◽  
Xuming Li ◽  
...  
Keyword(s):  
Functional Categories ◽  
Gene Expressions ◽  
Context Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Genome Context Analysis ◽  
Genome Context ◽  
And Function

Background: Riboswitches are structured elements that usually reside in the noncoding regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene expressions. To date, more than twenty different classes of riboswitches have been characterized to sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal ions, etc. </P><P> Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and function analyses of the corresponding downstream genes in prokaryotes. Results: In this study, we have completed a genome context analysis of 27 riboswitches to elucidate their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079 prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was applied to predict and classify the possible functions of corresponding downstream genes of these riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG functional categories, in which the two main clusters &quot;coenzyme metabolism [H]&quot; and &quot;amino acid transport and metabolism [E]&quot; were the most significantly enriched. Conclusion: Riboswitches are found to be widespread in bacteria, among which three main classes of TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of functions were associated with the corresponding downstream genes, suggesting that a wide extend of regulatory roles were mediated by these riboswitches in prokaryotes.

scholarly journals Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico

2019 ◽  
Author(s):  
Takahiro Nakamura ◽  
Muhamad Fahmi ◽  
Jun Tanaka ◽  
Kaito Seki ◽  
Yukihiro Kubota ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Glycoside Hydrolases ◽  
Data Driven ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Class 1 ◽  
And Function ◽  
Multicellular Organisms ◽  
Disordered Regions

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy, and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3), and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.

scholarly journals Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

2020 ◽  
Author(s):  
Hongwei Zhang ◽  
Xinxia Liang ◽  
Shuo Zhou ◽  
Haibo Wang
Keyword(s):  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Suppressor Gene ◽  
Pcr Analysis ◽  
Genome Wide Analysis ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Mads Box Gene ◽  
And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

scholarly journals Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico

2019 ◽  
Vol 20 (24) ◽  
pp. 6290 ◽  
Author(s):  
Takahiro Nakamura ◽  
Muhamad Fahmi ◽  
Jun Tanaka ◽  
Kaito Seki ◽  
Yukihiro Kubota ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Glycoside Hydrolases ◽  
Data Driven ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Class 1 ◽  
And Function ◽  
Multicellular Organisms ◽  
Disordered Regions

Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.

scholarly journals Energetic Evolution of Cellular Transportomes

2017 ◽  
Author(s):  
Behrooz Darbani ◽  
Douglas B. Kell ◽  
Irina Borodina
Keyword(s):  
Ion Channels ◽  
Bacterial Species ◽  
Living Cells ◽  
Energetic Efficiency ◽  
Cellular Functions ◽  
Transporter Proteins ◽  
Genome Wide Analysis ◽  
Solute Carriers ◽  
Genome Wide ◽  
A Genome

ABSTRACTTransporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

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