scholarly journals Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10312
Author(s):  
Ting-Ting Zhang ◽  
Yi-Kun Hou ◽  
Ting Yang ◽  
Shu-Ya Zhang ◽  
Ming Yue ◽  
...  
Keyword(s):  
Structural Variation ◽  
Gene Loss ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Comprehensive Understanding ◽  
Transfer Rnas ◽  
Evolutionary Aspect ◽  
Evolutionary Pattern ◽  
Information Level ◽  
Key Participants

Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.

scholarly journals Compositional diversity and evolutionary pattern of coronavirus accessory proteins

2020 ◽  
Author(s):  
Jingzhe Shang ◽  
Na Han ◽  
Ziyi Chen ◽  
Yousong Peng ◽  
Liang Li ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Regulatory Sequence ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Reading Frame ◽  
Evolutionary Pattern ◽  
Host Interaction ◽  
Sequence Recognition ◽  
Compositional Diversity

Abstract Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.

scholarly journals A novel thermostable aspartic protease fromTalaromyces leycettanusand its specific autocatalytic activation through an intermediate transition state

2019 ◽  
Author(s):  
Yujie Guo ◽  
Tao Tu ◽  
Yaxin Ren ◽  
Yaru Wang ◽  
Yingguo Bai ◽  
...  
Keyword(s):  
Specific Pattern ◽  
Aspartic Protease ◽  
Activation Process ◽  
Evolutionary Analysis ◽  
The Novel ◽  
Mature Protein ◽  
Aspartic Proteases ◽  
Family Based ◽  
Two Stages ◽  
Protease Precursor

ABSTRACTAspartic proteases exhibit optimum enzyme activity under acidic condition and have been extensively used in food, fermentation and leather industries. In this study, a novel aspartic protease precursor (proTlAPA1) fromTalaromyces leycettanuswas identified and successfully expressed inPichia pastoris. Subsequently, the auto-activation processing of the zymogen proTlAPA1 was studied by SDS-PAGE and N-terminal sequencing, under different processing conditions.TlAPA1 shared the highest identity of 70.3 % with the aspartic endopeptidase fromByssochlamys spectabilis(GAD91729) and was classified into a new subgroup of the aspartic protease A1 family, based on evolutionary analysis. MatureTlAPA1 protein displayed an optimal activity at 60 °C and remained stable at temperatures of 55 °C and below, indicating the thermostable nature ofTlAPA1 aspartic protease. During the auto-activation processing of proTlAPA1, a 45 kDa intermediate was identified that divided the processing mechanism into two steps: formation of intermediates, and activation of the mature protein (TlAPA1). The former step was completely induced by pH of the buffer, while the latter process depended on protease activity. The discovery of the novel aspartic proteaseTlAPA1 and study of its activation process will contribute to a better understanding of the mechanism of aspartic proteases auto-activation.IMPORTANCEThe novel aspartic proteaseTlAPA1 was identified fromT. leycettanusand expressed as a zymogen (proTlAPA1) inP. pastoris. Enzymatic characteristics of the mature protein were studied and the specific pattern of zymogen conversion was described. The auto-activation processing of proTlAPA1 proceeded in two stages and an intermediate was identified in this process. These results describe a new subgroup of aspartic protease A1 family and provide insights into a novel mode of activation processing in aspartic proteases.

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