Conserved Consensus Sequence Research Articles

Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Family in Response to Various Abiotic Stresses in Coconut (Cocos nucifera L.).

Abiotic stresses such as nitrogen deficiency, drought, and salinity significantly impact coconut production, yet the molecular mechanisms underlying coconut's response to these stresses are poorly understood. MYB proteins, a large and diverse family of transcription factors (TF), play crucial roles in plant responses to various abiotic stresses, but their genome-wide characterization and functional roles in coconut have not been comprehensively explored. This study identified 214 CnMYB genes (39 1R-MYB, 171 R2R3-MYB, 2 3R-MYB, and 2 4R-MYB) in the coconut genome. Phylogenetic analysis revealed that these genes are unevenly distributed across the 16 chromosomes, with conserved consensus sequences, motifs, and gene structures within the same subgroups. Synteny analysis indicated that segmental duplication primarily drove CnMYB evolution in coconut, with low nonsynonymous/synonymous ratios suggesting strong purifying selection. The gene ontology (GO) annotation of protein sequences provided insights into the biological functions of the CnMYB gene family. CnMYB47/70/83/119/186 and CnMYB2/45/85/158/195 were identified as homologous genes linked to nitrogen deficiency, drought, and salinity stress through BLAST, highlighting the key role of CnMYB genes in abiotic stress tolerance. Quantitative analysis of PCR showed 10 CnMYB genes in leaves and petioles and found that the expression of CnMYB45/47/70/83/85/119/186 was higher in 3-month-old than one-year-old coconut, whereas CnMYB2/158/195 was higher in one-year-old coconut. Moreover, the expression of CnMYB70, CnMYB2, and CnMYB2/158 was high under nitrogen deficiency, drought, and salinity stress, respectively. The predicted secondary and tertiary structures of three key CnMYB proteins involved in abiotic stress revealed distinct inter-proteomic features. The predicted interaction between CnMYB2/158 and Hsp70 supports its role in coconut's drought and salinity stress responses. These results expand our understanding of the relationships between the evolution and function of MYB genes, and provide valuable insights into the MYB gene family's role in abiotic stress in coconut.

GSK3β phosphorylates Six1 transcription factor and regulates its APC/CCdh1 mediated proteosomal degradation

Sine oculis homeobox homolog 1 (Six1) is a developmentally important transcription factor that regulates cellular proliferation, apoptosis, and dissemination during embryogenesis. Six1 overexpression as reported in multiple cancers modulates expression of a repertoire of its target genes causing an increase in proliferation, metastasis and survival of cancer cells. Six1 exists as a cell cycle regulated nuclear phosphoprotein and its cellular turnover is regulated by APC/C (Anaphase promoting complex / Cyclosome) complex mediated proteolysis. However, the kinases that regulate Six1 proteolysis have not been identified and the mechanistic details that cause its overproduction in various cancers are lacking. Here, we report that Six1 is a physiological GSK3β substrate. GSK3β interacts with Six1 and phosphorylates it at Ser221 within the conserved consensus sequence in its carboxy terminus. Using pharmacological inhibition, siRNA mediated knockdown and protein overexpression of GSK3β; we show that GSK3β regulates Six1 protein stability. Pulse chase analysis of Six1 revealed that GSK3β regulates its ubiquitin proteolysis such that Six1 phosphomimicking mutant (Six1S221E) for Ser221 site had dramatically increased half-life than its phosphodeficient (Six1S221A) and wild type variants. Furthermore, we demonstrate that GSK3β rescues Six1 from APC dependent proteolysis by regulating its binding with APC/C co-activator protein Cdh1. Importantly, strong positive correlation exists between GSK3β and Six1 protein levels throughout the cell cycle and in multiple cancers indicating that GSK3β activation may in part contribute to Six1 overproduction in a subset of human cancers.

Identification and characterization of a novel Cytorhabdovirus associated with goji berry (Lycium barbarum L.) crinkle disease.

Goji berry (Lycium barbarum L.) is a traditional Chinese herbal medicinal plant that is extensively cultivated in the arid and semiarid regions of northwest China. In this study, a novel cytorhabdovirus, tentatively named "goji cytorhabdovirus A (GCVA)," was identified from the goji berry plant exhibiting leaf crinkle symptoms through high-throughput sequencing (HTS). GCVA contains a linear, negative sense single-stranded RNA genome of 14,812 nucleotides and encodes six open reading frames in the order of 3' leader-N-P-P4-M-G-L-5' trailer. The genome of GCVA shares the highest nucleotide (nt) identity of 65.80% (16% query coverage) with yerba mate virus A (YmVA) (NC_076472). The N and L proteins also share low amino acid (aa) identities (<35.42 and < 41.23%, respectively) with known cytorhabdoviruses. Typical features of the viruses in the genus Cytorhabdovirus include a highly conserved consensus sequence in the intergenic regions and extensive complementation of the 5' non-coding trailer and the 3' leader. These features were also found in GCVA. These data in combination with a phylogenetic analysis that was based on the aa sequences of the N and L proteins support the proposal that GCVA is a new species in the genus Cytorhabdovirus.

African ZIKV lineage fails to sustain infectivity in an in vitro mimetic urban cycle.

Zika virus (ZIKV) is an arbovirus maintained in nature in two distinct cycles of transmission: urban and sylvatic. Each cycle includes specific vertebrate and invertebrate hosts, and through alternate infections, a conserved consensus sequence is maintained that might vary depending on the cycle. The current study aimed to investigate the ability of ZIKVAF and ZIKVBR to maintain an infectious cycle by alternating passages in cells mimicking the urban (UC) and semi-sylvatic (SC) cycles. The complete genome of the original inoculum and the last passages for each cycle were sequenced by Sanger. Ten passages were performed, as planned, for ZIKVBR UC, ZIKVAF SC, and ZIKVBR SC. ZIKVBR SC showed significant variation in viral titers along the passages, suggesting that the virus is not well adapted to the non-human primate host. ZIKVAF passage in UC was abrogated in the third passage, showing the inability of the African lineage to sustain cycles in human cells, suggesting a low capacity to establish an urban cycle. Several mutations were found in both strains along the passages, but not occurring at equivalent positions. Further studies are needed to elucidate whether any of these specific mutations affect viral fitness. ZIKV strains behave differently in artificial transmission cycles in vitro: Brazilian ZIKV was able to establish urban and semi-sylvatic cycles in vitro. African ZIKV proved unable to cycle among human and mosquito cells and is compatible only with the semi-sylvatic cycle. The main mutations arose in the NS2A region after artificial transmission cycles for both ZIKV strains but not at equivalent positions.

Comparative Analysis of DNA-Polymerases from Family A as a Tool to Search for Enzymes with New Properties

DNA-polymerases catalyze DNA synthesis during DNA replication, repair, and recombination. A number of DNA-polymerases, such as the Taq enzyme from Thermus aquaticus, are used in various applications of molecular biology and biotechnology, in particular as DNA amplification tools. However, the efficiency of these enzymes depends on factors such as DNA origin, primer composition, template length, GC-content, and the ability to form stable secondary structures. Such limitations in the use of currently known DNA-polymerases leave the problem of searching for new enzymes with improved properties. This review summarizes the main structural and molecular-kinetic features of the functioning of DNA-polymerases belonging to the structural family A, including Taq polymerase. A phylogenetic analysis of these enzymes was carried out, which made it possible to establish a highly conserved consensus sequence containing 62 amino acid residues distributed over the structure of the enzyme. A comparative analysis of these amino acid residues among poorly studied DNA-polymerases revealed 7 enzymes that potentially have the properties necessary for their use for DNA amplification.

Comparative Analysis of Family A DNA-Polymerases as a Searching Tool for Enzymes with New Properties

DNA polymerases catalyze DNA synthesis during DNA replication, repair, and recombination. A number of DNA polymerases, such as the Taq enzyme from Thermus aquaticus, are used in various applications of molecular biology and biotechnology, in particular as DNA amplification tools. However, the efficiency of these enzymes depends on factors such as DNA origin, primer composition, template length, GC-content, and the ability to form stable secondary structures. These limitations in the use of currently known DNA polymerases lead to the search for new enzymes with improved properties. This review summarizes the main structural and molecular-kinetic features of the functioning of DNA-polymerases belonging to structural family A, including Taq polymerase. A phylogenetic analysis of these enzymes was carried out, which made it possible to establish a highly conserved consensus sequence containing 62 amino acid residues distributed over the structure of the enzyme. A comparative analysis of these amino acid residues among poorly studied DNA-polymerases revealed 7 enzymes that potentially have the properties necessary for use in DNA amplification.

The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice.

Control over gene expression is exerted, in multiple stages of spermatogenesis, at the post-transcriptional level by RNA binding proteins (RBPs). We identify here an essential role in mammalian spermatogenesis and male fertility for ‘RNA binding protein 46’ (RBM46). A highly evolutionarily conserved gene, Rbm46 is also essential for fertility in both flies and fish. We found Rbm46 expression was restricted to the mouse germline, detectable in males in the cytoplasm of premeiotic spermatogonia and meiotic spermatocytes. To define its requirement for spermatogenesis, we generated Rbm46 knockout (KO, Rbm46-/-) mice; although male Rbm46-/- mice were viable and appeared grossly normal, they were infertile. Testes from adult Rbm46-/- mice were small, with seminiferous tubules containing only Sertoli cells and few undifferentiated spermatogonia. Using genome-wide unbiased high throughput assays RNA-seq and ‘enhanced crosslinking immunoprecipitation’ coupled with RNA-seq (eCLIP-seq), we discovered RBM46 could bind, via a U-rich conserved consensus sequence, to a cohort of mRNAs encoding proteins required for completion of differentiation and subsequent meiotic initiation. In summary, our studies support an essential role for RBM46 in regulating target mRNAs during spermatogonia differentiation prior to the commitment to meiosis in mice.

Infection-induced molecular pattern recognition proteins in larvae of Protaetia brevitarsis seulensis (Coleoptera: Cetoniidae)

We cloned and sequenced full-length peptidoglycan recognition protein (PGRP)-like cDNAs, named PS PGRP-SA(a)-like, PS PGRP-SA(b)-like, PS PGRP-SB1-like and PS PGRP-SC-like, from Protaetia brevitarsis seulensis. The amino acid sequences of PS PGRPs share 32.03-47.93% homology with those of PGRP family members in insects and mammals, including humans. We identified a conserved consensus sequence for amidase activity (His; H-Tyr; Y-His; H-Thr; T-Cys; C) and residues for binding peptidoglycan (PGN), one of the major bacterial cell wall components, including Asp (D) and Phe (F) for Lys-type PGN; and Gly(G), Trp (W) and Arg (R) for DAP-type PGN. The topological structures of PS PGRP-SA(a)-like, PS PGRP-SA(b)-like and PS PGRP-SC-like proteins are structurally similar to those of Drosophila melanogaster PGRP-SA, which has three &#945;-helices and six &#946;-strands. The &#946;-strands are located in a central region and helix &#945;1 on the back and peripheral &#945;2 and &#945;3 helices are on the front. The three &#945;-helices and six &#946;-strands are also present in PS PGRP-SB1-like, but the topological structure differs from that of typical PGRP. Significantly increased levels of PS PGRP-SA (a)-like and PS PGRP-SA (b)-like mRNA were recorded when Gram-positive bacteria or yeast cells were injected into larvae. PS PGRP-SB1-like mRNA levels were up-regulated by infection by all three pathogens; however, expression of PS PGRP-SC-like mRNA was increased 20- or 30-fold only shortly after injection with Gram-negative bacteria.

Eogt-catalyzed &lt;i&gt;O&lt;/i&gt;-GlcNAcylation

O-GlcNAcylation is critical in human physiology. The dysregulation of O-GlcNAcylation on various intracellular proteins impacts cardiovascular diseases, the immune system, type 2 diabetes, neurodegeneration diseases, and cancers. In the past decade, extracellular O-GlcNAcylation was discovered from the conserved epidermal growth factor-like (EGF) domain in Drosophila and mammals. Extracellular O-GlcNAcylation is catalyzed by EGF domain O-GlcNAc transferase (EOGT) in the endoplasmic reticulum, and, unlike intracellular O-GlcNAcylation, it is further elongated with galactose and sialic acid in the Golgi apparatus. In this review, we retrospect the studies addressing the catalysis of EOGT, the conserved consensus sequence, the impacts of abnormal extracellular O-GlcNAcylation, and the diseases related to EOGT mutation.

Cloning and identification of a new repressor of 3,17β-Hydroxysteroid dehydrogenase of Comamonas testosteroni.

3,17β-hydroxysteroid dehydrogenase (3,17β-HSD) is a key enzyme in the metabolic pathway for steroid compounds catabolism in Comamonas testosteroni. Tetracycline repressor (TetR) family, repressors existing in most microorganisms, may play key roles in regulating the expression of 3,17β-HSD. Previous reports showed that three tetR genes are located in the contig58 of C. testosteroni ATCC 11996 (GenBank: AHIL01000049.1), among which the first tetR gene encoded a potential repressor of 3,17β-HSD by sensing environmental signals. However, whether the other proposed tetR genes act as repressors of 3,17β-HSD are still unknown. In the present study, we cloned the second tetR gene and analyzed the regulatory mechanism of the protein on 3,17β-HSD using electrophoretic mobility shift assay (EMSA), gold nanoparticles (AuNPs)-based assay, and loss-of-function analysis. The results showed that the second tetR gene was 660-bp, encoding a 26 kD protein, which could regulate the expression of 3,17β-HSD gene via binding to the conserved consensus sequences located 1100-bp upstream of the 3,17β-HSD gene. Furthermore, the mutant strain of C. testosteroni with the second tetR gene knocked-out mutant expresses good biological genetic stability, and the expression of 3,17β-HSD in the mutant strain is slightly higher than that in the wild type under testosterone induction. The second tetR gene acts as a negative regulator in 3,17β-HSD expression, and the mutant has potential application in bioremediation of steroids contaminated environment.

Characterization of tolloid-mediated cleavage of the GDF8 procomplex.

Growth differentiation factor 8 (GDF8), a.k.a. myostatin, is a member of the larger TGFβ superfamily of signaling ligands. GDF8 has been well characterized as a negative regulator of muscle mass. After synthesis, GDF8 is held latent by a noncovalent complex between the N-terminal prodomain and the signaling ligand. Activation of latent GDF8 requires proteolytic cleavage of the prodomain at residue D99 by a member of the tolloid family of metalloproteases. While tolloid proteases cleave multiple substrates, they lack a conserved consensus sequence. Here, we investigate the tolloid cleavage site of the GDF8 prodomain to determine what residues contribute to tolloid recognition and subsequent proteolysis. Using sequential alanine mutations, we identified several residues adjacent to the scissile bond, including Y94, that when mutated, abolish tolloid-mediated activation of latent GDF8. Using the astacin domain of Tll1 (Tolloid Like 1) we determined that prodomain mutants were more resistant to proteolysis. Purified latent complexes harboring the prodomain mutations, D92A and Y94A, impeded activation by tolloid but could be fully activated under acidic conditions. Finally, we show that co-expression of GDF8 WT with prodomain mutants that were tolloid resistant, suppressed GDF8 activity. Taken together our data demonstrate that residues towards the N-terminus of the scissile bond are important for tolloid-mediated activation of GDF8 and that the tolloid-resistant version of the GDF8 prodomain can function dominant negative to WT GDF8.

Interactomic affinity profiling by holdup assay: Acetylation and distal residues impact the PDZome-binding specificity of PTEN phosphatase.

Protein domains often recognize short linear protein motifs composed of a core conserved consensus sequence surrounded by less critical, modulatory positions. PTEN, a lipid phosphatase involved in phosphatidylinositol 3-kinase (PI3K) pathway, contains such a short motif located at the extreme C-terminus capable to recognize PDZ domains. It has been shown that the acetylation of this motif could modulate the interaction with several PDZ domains. Here we used an accurate experimental approach combining high-throughput holdup chromatographic assay and competitive fluorescence polarization technique to measure quantitative binding affinity profiles of the PDZ domain-binding motif (PBM) of PTEN. We substantially extended the previous knowledge towards the 266 known human PDZ domains, generating the full PDZome-binding profile of the PTEN PBM. We confirmed that inclusion of N-terminal flanking residues, acetylation or mutation of a lysine at a modulatory position significantly altered the PDZome-binding profile. A numerical specificity index is also introduced as an attempt to quantify the specificity of a given PBM over the complete PDZome. Our results highlight the impact of modulatory residues and post-translational modifications on PBM interactomes and their specificity.

Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo.

Heat-shock proteins (HSP) are conserved chaperones crucial for protein degradation, maturation, and refolding. These adenosine triphosphate dependent chaperones were classified based on their molecular mass that ranges between 10–100 kDA, including; HSP10, HSP40, HSP70, HSP90, HSPB1, HSPD, and HSPH1 family. HSPs are essential for cellular responses and imperative for protein homeostasis and survival under stress conditions. This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level. Physiochemical properties, multiple sequence alignment, and phylogenetic analysis were performed for 64 HSP genes in the Bubalus bubalis genome. Four genes were identified as belonging to the HSP90 family, 10 to HSP70, 39 to HSP40, 8 to HSPB, one for each HSPD, HSPH1, and HSP10, respectively. The aliphatic index was higher for HSP90 and HSP70 as compared to the HSP40 family, indicating their greater thermostability. Grand Average of hydropathicity Index values indicated the hydrophilic nature of HSP90, HSP70, and HSP40. Multiple sequence alignment indicated the presence of highly conserved consensus sequences that are plausibly significant for the preservation of structural integrity of proteins. In addition, this study has expanded our current knowledge concerning the genetic diversity and phylogenetic relatedness of HSPs of buffalo with other mammalian species. The phylogenetic tree revealed that buffalo is more closely related to Capra hircus and distantly associated with Danio rerio. Our findings provide an understanding of HSPs in buffalo at the molecular level for the first time. This study highlights functionally important HSPs and indicates the need for further investigations to better understand the role and mechanism of HSPs.

Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in Corynebacterium glutamicum ATCC 13032.

Corynebacterium glutamicum ATCC 13032 harbors five sigma subunits of RNA polymerase belonging to Group IV, also called extracytoplasmic function (ECF) σ factors. These factors σC, σD, σE, σH, and σM are mostly involved in stress responses. The role of σD consists in the control of cell wall integrity. The σD regulon is involved in the synthesis of components of the mycomembrane which is part of the cell wall in C. glutamicum. RNA sequencing of the transcriptome from a strain overexpressing the sigD gene provided 29 potential σD-controlled genes and enabled us to precisely localize their transcriptional start sites. Analysis of the respective promoters by both in vitro transcription and the in vivo two-plasmid assay confirmed that transcription of 11 of the tested genes is directly σD-dependent. The key sequence elements of all these promoters were found to be identical or closely similar to the motifs -35 GTAACA/G and -10 GAT. Surprisingly, nearly all of these σD-dependent promoters were also active to a much lower extent with σH in vivo and one (Pcg0607) also in vitro, although the known highly conserved consensus sequence of the σH-dependent promoters is different (-35 GGAAT/C and -10 GTT). In addition to the activity of σH at the σD-controlled promoters, we discovered separated or overlapping σA- or σB-regulated or σH-regulated promoters within the upstream region of 8 genes of the σD-regulon. We found that phenol in the cultivation medium acts as a stress factor inducing expression of some σD-dependent genes. Computer modeling revealed that σH binds to the promoter DNA in a similar manner as σD to the analogous promoter elements. The homology models together with mutational analysis showed that the key amino acids, Ala 60 in σD and Lys 53 in σH, bind to the second nucleotide within the respective -10 promoter elements (GAT and GTT, respectively). The presented data obtained by integrating in vivo, in vitro and in silico approaches demonstrate that most of the σD-controlled genes also belong to the σH-regulon and are also transcribed from the overlapping or closely located housekeeping (σA-regulated) and/or general stress (σB-regulated) promoters.

The S6 gate in regulatory Kv6 subunits restricts heteromeric K+ channel stoichiometry.

The Shaker-like family of voltage-gated K+ channels comprises four functionally independent gene subfamilies, Shaker (Kv1), Shab (Kv2), Shaw (Kv3), and Shal (Kv4), each of which regulates distinct aspects of neuronal excitability. Subfamily-specific assembly of tetrameric channels is mediated by the N-terminal T1 domain and segregates Kv1-4, allowing multiple channel types to function independently in the same cell. Typical Shaker-like Kv subunits can form functional channels as homotetramers, but a group of mammalian Kv2-related genes (Kv5.1, Kv6s, Kv8s, and Kv9s) encodes subunits that have a "silent" or "regulatory" phenotype characterized by T1 self-incompatibility. These channels are unable to form homotetramers, but instead heteromerize with Kv2.1 or Kv2.2 to diversify the functional properties of these delayed rectifiers. While T1 self-incompatibility predicts that these heterotetramers could contain up to two regulatory (R) subunits, experiments show a predominance of 3:1R stoichiometry in which heteromeric channels contain a single regulatory subunit. Substitution of the self-compatible Kv2.1 T1 domain into the regulatory subunit Kv6.4 does not alter the stoichiometry of Kv2.1:Kv6.4 heteromers. Here, to identify other channel structures that might be responsible for favoring the 3:1R stoichiometry, we compare the sequences of mammalian regulatory subunits to independently evolved regulatory subunits from cnidarians. The most widespread feature of regulatory subunits is the presence of atypical substitutions in the highly conserved consensus sequence of the intracellular S6 activation gate of the pore. We show that two amino acid substitutions in the S6 gate of the regulatory subunit Kv6.4 restrict the functional stoichiometry of Kv2.1:Kv6.4 to 3:1R by limiting the formation and function of 2:2R heteromers. We propose a two-step model for the evolution of the asymmetric 3:1R stoichiometry, which begins with evolution of self-incompatibility to establish the regulatory phenotype, followed by drift of the activation gate consensus sequence under relaxed selection to limit stoichiometry to 3:1R.

Estrogen Receptor α- and β-Interacting Proteins Contain Consensus Secondary Structures: An Insilico Study

Background: Estrogen receptor (ER)α and ERβ are ligand-activated transcription factors that regulate gene expression by binding to estrogen-responsive elements and interacting with several coregulators through protein-protein interactions. Usually, these coregulators bind to the various conserved and functional domains of the receptor through a consensus LXXLL sequence, although variations can be found. The interaction of receptor domains and the consensus motif can be a possible target for nuclear receptor (NR) pharmacology, since modifications in these are responsible for possible pathogenesis of various diseases. Purpose: The present study focuses on the secondary structure and conserved domains of the ERα and ERβ interacting proteins, using bioinformatics tools and their relation to the function of the coregulators. Methods: Bioinformatics-based prediction tools like STRING, PSIPRED, PROTPARAM and Conserved Domain Database (CDD) were used. The prediction tools utilized in this study basically determines the characteristics of a possible coregulator by using an already existing protein as a template and determines the presence of any conserved consensus sequence. Coregulators have been enlisted with the help of NCBI, STRING and iHOP. The secondary structures were analyzed using PSIPRED and conserved domains were determined using CDD. Results: The analysis of the structure has shown the presence of conserved domains and homology between the various coregulators. Each interacting protein contains conserved domains like the nuclear coactivators’ domain, the helix-loop-helix domain and the SRC domain. Conclusion: Such studies give the characteristic features of ERα and ERβ interacting proteins and maybe useful to determine their family and uses in NR pharmacology in health and diseases.

Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa.

Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNASer found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O. sativa and to our knowledge, this is the smallest gene of eukaryotic lineage reported so far. Analyses revealed the presence of several novel/pseudo tRNA genes in O. sativa which are reported for the first time. Multiple sequence alignment of tRNAs revealed the presence of family specific conserved consensus sequences. Functional study of these novel tRNA and family specific conserved consensus sequences will be crucial to decipher their importance in biological events. The rate of transition of O. sativa tRNA was found to be higher than the rate of transversion. Evolutionary study revealed, O. sativa tRNAs were evolved from the lineages of multiple common ancestors. Duplication and loss study of tRNAs genes revealed, majority of the O. sativa tRNA were duplicated and 17 of them were found to be undergone loss during the evolution. Orthology and paralogy study showed, the majority of O. sativa tRNA were paralogous and only a few of tRNASer were found to contain orthologous tRNAs.

Construction and immunogenicity of a recombinant swinepox virus expressing a multi-epitope peptide for porcine reproductive and respiratory syndrome virus

To characterize neutralizing mimotopes, phages were selected from a 12-mer phage display library using three anti-porcine reproductive and respiratory syndrome virus (PRRSV) neutralizing monoclonal antibodies: (1) A1; (2) A2; and (3) A7. Of these, A2 and A7 recognize the mimotope, P2, which contains the SRHDHIH motif, which has conserved consensus sequences from amino acid positions 156 to 161 in the N-terminal ectodomain of GP3. The artificial multi-epitope gene, mp2, was designed by combining three repeats of the mimotope P2. The resulting sequence was inserted into the swinepox virus (SPV) genome to construct a recombinant swinepox virus (rSPV-mp2). The rSPV-mp2 was able to stably express the multi-epitope peptide, mP2, in vitro. The rSPV-mp2 immunized pigs exhibited a significantly shorter fever duration compared with the wtSPV treated group (P < 0.05). There was an enhanced humoral and cellular immune response, decreased number of PRRSV genomic copies, and a significant reduction in the gross lung pathology (P < 0.05) was observed following PRRSV infection in rSPV-mp2-immunized animals. The results suggest that the recombinant rSPV-mp2 provided pigs with significant protection against PRRSV infection.

Genome-wide analysis of the family 1 glycosyltransferases in cotton.

Family 1 GT, designated as UGT, is the largest and most functionally important multigene family in the plant kingdom. In this study, we carried out a genome-wide identification, analysis, and comparison of 142, 146, and 196 putative UGTs from Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum, respectively. All members present the 44 amino-acid conserved consensus sequence termed the plant secondary product glycosyltransferase motif. According to the phylogenetic relationship among the cotton UGT proteins and those from other species, GrUGTs and GaUGTs could be classified into 16 major phylogenetic groups (A-P), whereas GhUGTs are classified into 15 major phylogenetic groups with a lack of group C. All cotton UGTs are dispersed throughout the chromosomes and are displayed in clusters with the same open reading frame orientation. The expansion of them appears to result from genome duplication and rearrangement. Two conserved introns, A and B, are detected in most of the intron-containing-UGTs in G. raimondii and G. arboreum, whereas only intron A is detected in the intron-containing-UGTs in G. hirsutum. Furthermore, expression patterns of the UGT genes in G. hirsutum wild type and its near isogenic fuzzless-lintless mutant at the stage of fiber initiation were analyzed using the RNA-seq data. Overall, this study not only deepens our understanding of the structure, phylogeny, evolution, and expression of cotton UGT genes, but also provides a solid foundation for further cloning and functional studies of the UGT family genes.

The Homologous Regions ofSpodoptera litura(Lepidoptera: Noctuidae) Nucleopolyhedrovirus II Have Both the Function as Origin of DNA Replication and Enhancer

In the genome sequence of the Spodoptera litura nucleopolyhedrovirus II (SpltNPVII), seven homologous regions (hrs), Sphr1-7, were identified. Each of them composed of three to eight 64-bp highly conserved sequences, and each contained a 24-bp imperfect palindrome. A transient expression assay demonstrated that the expression of SpltNPVII-ie1 promoter-driven luciferase gene was enhanced between 3- and 13-fold by infection of SpltNPVII in Spli221 cells. Real-time polymerase chain reaction confirmed each of seven hrs could function as origin (ori) of viral DNA replication. This suggests that these hrs are bifunctional, having both ori and enhancer activities for transcription. In addition, the potential of seven hrs as origins had a significantly positive correlation with the number of their palindromes (r = 0.847, Sig: 0.016 < 0.05), and enhancer efficiency had a significantly positive correlation with the number of characteristic motifs (r = 0.893, Sig: 0.007 < 0.01). The efficiency of replication and enhancement of each hr both increased with increasing total numbers of palindromes, repeat sequences, and characteristic motifs. In addition, a single 64-bp highly conserved consensus sequence cannot very good support to the function as origin and enhancer, and require the assistance of other cis-elements in hrs.