Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.

HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.

Plant MicroRNA Potential in Targeting Sars-CoV-2 Genome Offering Efficient Antiviral MiRNA-Based Therapies.

BACKGROUND: In 2019, severe acute respiratory coronavirus II (or SARS-COV-2) emerged in Wuhan, China, rapidly becoming a global pandemic. Coronavirus genus (Coronaviridae) has the largest single-stranded positive-sense RNA genome (~30 kb) among the human infected single-stranded RNA viruses. OBJECTIVES: For the study of active therapeutic plant-derived miRNA(s), it may be possible to uptake the miRNAs and their biological role in the host cell. In this study, we bioinformatically searched plant miRNAs that can potentially interact with the Sars-CoV-2 genome within the 3'- UTR region and have prompt antiviral activity. MATERIALS AND METHODS: We searched the plant miRNAs that target the 3'-UTR flanking region of the Sars-CoV-2 genome by employing the RNAHybrid, RNA22, and STarMir miRNA/target prediction tools. RESULTS: The RNAHybrid algorithm found 63 plant miRNAs having hybridization energy with less or equal to -25 kcal.mol-1. Besides, RNA22 and STarMir tools identified eight interactions between the plant miRNAs and the targeted RNA sequence. pvu-miR159a. 2 and sbi-miR5387b were predicted as the most effectively interacting miRNAs in targeting the 3'-UTR sequence, not only by the RNA22 tool but also by the STarMir tool at the same position. However, the GC content of the pvumiR159a. 2 is 55% instead of sbi-miR5387b, which is a GC enriched sequence (71.43%) that may activate TLR receptors. CONCLUSION: In our opinion, they are potent plant-derived miRNA candidates that have a great chance of targeting the Sars-CoV-2 genome in the 3'-UTR region in vitro. Therefore, we propose pvu-miR159a.2 for studying antiviral miRNA-based therapies without any essential side effects in vivo.

Comparative phylogeny and evolutionary analysis of Dicer-like protein family in two plant monophyletic lineages.

BACKGROUND: Small RNAs (sRNAs) that do not get untranslated into proteins exhibit a pivotal role in the expression regulation of their cognate gene(s) in almost all eukaryotic lineages, including plants. Hitherto, numerous protein families such as Dicer, a unique class of Ribonuclease III, have been reported to be involved in sRNAs processing pathways and silencing. In this study, we aimed to investigate the phylogenetic relationship and evolutionary history of the DCL protein family. RESULTS: Our results illustrated the DCL family of proteins grouped into four main subfamilies (DCLs 1-4) presented in either Eudicotyledons or Liliopsids. The accurate observation of the phylogenetic trees supports the independent expansion of DCL proteins among the Eudicotyledons and Liliopsids species. They share the common origin, and the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsids split from their ancestral DCL. In addition, shreds of evidence revealed that the divergence happened when multicellularization started and since the need for complex gene regulation considered being a necessity by organisms. At that time, they have evolved independently among the monophyletic lineages. The other finding was that the combination of DCL protein subfamilies bears several highly conserved functional domains in plant species that originated from their ancestor architecture. The conservation of these domains happens to be both lineage-specific and inter lineage-specific. CONCLUSIONS: DCL subfamilies (i.e., DCL1-DCL4) distribute in their single clades after diverging from their common ancestor and before emerging into higher plants. Therefore, it seems that the main duplication events for the formation of the DCL subfamilies occurred before the Eudicotyledons/Liliopsida split and before the appearance of moss, and after the single-cell green algae. We also observed the same trends among the main DCL subfamilies from functional unit composition and architecture. Despite the long evolutionary course from the divergence of Liliopsida lineage from the Eudicotyledons, a significant diversifying force to domain composition and orientation was absent. The results of this study provide a deeper insight into DCL protein evolutionary history and possible sequence and structural relationships between DCL protein subfamilies in the main higher plant monophyletic lineages; i.e., Eudicotyledons and Liliopsida.

Plant RNA-mediated gene regulatory network.

Not all transcribed RNAs are protein-coding. Some non-coding RNAs (ncRNAs) seem to be non-functional and are resulted from spurious transcription. Many others have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several ncRNAs, as major elements, regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. RNA-mediated gene regulation machinery is evolutionarily ancient and pretty complex. In this review, the current knowledge in the field of RNA-mediated gene silencing have been summarized.

Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics.

Cytogenetics is concerned with the structure and number of chromosomes (Karyotyping) and their abnormalities not only in congenital but also in acquired genetic disorders. Chromosomal abnormalities can form when there is an error occurred in chromosome number and, or their structural changes. Such changes happen by itself or inductively by environmental agents like chemical reagents, radiation, etc. Cytogenetics techniques used to understand chromosomal disorders and their relationship to health and disease provide not only valuable clues about chromosome breakage and DNA repair mechanisms but also a more proper understanding of their relationship to cause various illnesses. In this sense, to evaluate chromosomal imbalance and rearrangement, alternative experimental methods have been expanded. Currently, Cytogenetics evolves into a multidimensional science that led to promoting both theoretically and technologically advanced molecular biology, flow cytometry, bioinformatics, and phylogeny. This study investigates the unique laboratory Cytogenetics methods, databases, algorithms, and software used molecular Cytogenetics to identify various chromosomal abnormalities.

DNA-protein interaction: identification, prediction and data analysis.

Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.

Computational Identification of MicroRNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.).

BACKGROUND: Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally. OBJECTIVE: In the present study, we report the results of a systemic search for identification of new miRNAs in B. rapa using homology-based ESTs (Expressed Sequence Tags) analysis and considering a series of fi ltration criteria. MATERIALS AND METHODS: Plant mature miRNA sequences were searched in non-protein coding ESTs registered in NCBI EST database. Zuker RNA folding algorithm was used to generate the secondary structures of the ESTs. Potential sequences were candidate as miRNA genes and characterized evolutionarily only and if only they fi t some described criteria. Also, the web tool psRNATarget was applied to predict candidate B. rapa miRNA targets. RESULTS: In this study, 10 novel miRNAs from B. rapa belonging to 6 miRNA families were identified using EST-based homology analysis by considering a series of fi ltration criteria. All potent miRNAs appropriate fold back structure. Several potential targets with known/unknown functions for these novel miRNAs were identified. The target genes mainly encode transcription factors, enzymes, DNA binding proteins, disease resistance proteins, carrier proteins and other biological processes. CONCLUSIONS: MicroRNA having diverse functions in plant species growth, development and evolution by posttranscriptionally regulating the levels of specific transcriptome so by effecting on their translation products. Research in miRNA led to the identification of many miRNAs and their regulating genes from diverse plant species.

Identification and Characterization of Novel miRNAs in Chlamydomonas reinhardtii by Computational Methods.

BACKGROUND: MicroRNAs (miRNAs) are endogenous small non-coding RNAs with 18-24 nucleotides in length, which have important roles in posttranscriptional gene regulation. The resemblance of miRNA biogenesis in unicellular green algae and those in plants suggests probable evolutionary conserved pathways. This conservation provides a ground towards prediction of new homologs via computational biology. METHODS: Here, conserved miRNA genes in Chlamydomonas reinhardtii and plants were examined through homology alignment. Previously known and unique plant miRNAs were BLASTed against expressed sequence tags (ESTs) and genomic survey sequences (GSSs) of C. reinhardtii. All candidate sequences with appropriate fold back structures were screened according to a series of miRNA filtering criteria. RESULTS: Homologous miRNAs (17), belonging to 9 miRNA gene families were predicted. Interestingly and for the first time, a miRNA family of genes was localized to chloroplast. Again and for the first time, here we report identification of C. reinhardtii miRNA orthologs in plants and animals. miRNA target genes were identified based on their sequence complementarities to the respective miRNAs using psRNATarget against C. reinhardtii, Unigene, and DFCI Gene Index (CHRGI). Totally, 152 potential target sites were identified. From the predicted miRNAs, 7 miRNAs had no target sequence in C. reinhardtii protein coding genes. CONCLUSION: Identifying miRNA and their target transcript(s) would be useful for other research concerned with the function and regulatory mechanisms of C. reinhardtii miRNAs and helps researchers to better understand the nature of its extensive metabolic flexibility and environmental compatibility to survive in distinct environmental niches and nutrient availability.

In vitro study on regeneration of Gladiolus grandiflorus corm calli as affected by plant growth regulators.

In this study, in vitro organogenesis of Gladiolus grandiflorus cultivar pink corm segments were evaluated by culturing corm calli in modified MS medium supplemented with 3% sucrose and 0.7% agar with different concentration of BAP (0, 1, 2 and 4 mg L(-1) medium) and NAA (0, 0.5, 1 and 2 mg L(-1) medium) in factorial experiment of Completely Randomized Design (CRD). In order to obtain Gladiolus calli, corm segments (Aprox. 5 x 5 x 1 mm in size) were kept in modified MS medium (Murashige and Skoog, 1962) that was supplemented with 1 mg L(-1) 2, 4-D, 3% sucrose and 0.7% agar. The results showed that increasing the concentration of BAP from 0 to 2 mg L(-1) medium simulated plantlet regeneration but no significantly effect was obtained on shoot and cormel organogenesis between 2 and 4 mg L(-1) BAP concentration in medium. Increasing of NAA content in media without BAP developed rootlet significantly. Interaction results showed that increasing BAP content against decreasing of NAA concentration stimulates the shoot and cormel proliferation.