High-Throughput Integrated Analyses for the Tyrosinase-Induced Melanogenesis: Microarray, Proteomics and Interactomics Studies

Tyrosinase-mediated melanogenesis in melanoma cells: Array comparative genome hybridization integrating proteomics and bioinformatics studies

We investigated the tyrosinase-associated melanogenesis in melanoma cells by using OMICS techniques. We characterized the chromosome copy numbers, including Chr 11q21 where the tyrosinase gene is located, from several melanoma cell lines (TXM13, G361, and SK-MEL-28) by using array CGH. We revealed that 11q21 is stable in TXM13 cells, which is directly related to a spontaneous high melanin pigment production. Meanwhile, significant loss of copy number of 11q21 was found in G361 and SK-MEL-28. We further profiled the proteome of TXM13 cells by LC-ESI-MSMS and detected more than 900 proteins, then predicted 11 hub proteins (YWHAZ; HSP90AA1; HSPA5; HSPA1L; HSPA9; HSP90B1; HSPA1A; HSPA8; FKSG30; ACTB; DKFZp686DQ972) by using an interactomic algorithm. YWHAZ (25% interaction in the network) is thought to be a most important protein as a linking factor between tyrosinase-triggered melanogenesis and melanoma growth. Bioinformatic tools were further applied for revealing various physiologic mechanisms and functional classification. The results revealed clues for the spontaneous pigmentation capability of TXM13 cells, contrary to G361 and SK-MEL-28 cells, which commonly have depigmentation properties during subculture. Our study comparatively conducted the genome-wide screening and proteomic profiling integrated interactomics prediction for TXM13 cells and suggests new insights for studying both melanogenesis and melanoma.

Dynamics of arginase gene evolution in metazoans

In the present study, a comprehensive analysis of the arginase gene family in metazoans was performed. A total of 126 arginase genes have been identified in 44 species. Phylogenetic analyses indicate that arginase genes consist of four groups. Conservative and divergent gene structures are found among the groups. The syntenies also exist in distantly related genomes among multiple species. Adaptive evolution shows that, while purifying selection may have been the main force driving the evolution of the arginases, some of critical sites responsible for the functional divergence may have been under positive selection. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the arginase gene family and of the function and evolution of this family in metazoans.

Computational prediction of protein-protein interactions of human tyrosinase

The various studies on tyrosinase have recently gained the attention of researchers due to their potential application values and the biological functions. In this study, we predicted the 3D structure of human tyrosinase and simulated the protein-protein interactions between tyrosinase and three binding partners, four and half LIM domains 2 (FHL2), cytochrome b-245 alpha polypeptide (CYBA), and RNA-binding motif protein 9 (RBM9). Our interaction simulations showed significant binding energy scores of -595.3 kcal/mol for FHL2, -859.1 kcal/mol for CYBA, and -821.3 kcal/mol for RBM9. We also investigated the residues of each protein facing toward the predicted site of interaction with tyrosinase. Our computational predictions will be useful for elucidating the protein-protein interactions of tyrosinase and studying its binding mechanisms.

Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods

In this paper, we re-annotated the genome of Pyrobaculum aerophilum str. IM2, particularly for hypothetical ORFs. The annotation process includes three parts. Firstly and most importantly, 23 new genes, which were missed in the original annotation, are found by combining similarity search and the ab initio gene finding approaches. Among these new genes, five have significant similarities with function-known genes and the rest have significant similarities with hypothetical ORFs contained in other genomes. Secondly, the coding potentials of the 1645 hypothetical ORFs are re-predicted by using 33 Z curve variables combined with Fisher linear discrimination method. With the accuracy being 99.68%, 25 originally annotated hypothetical ORFs are recognized as non-coding by our method. Thirdly, 80 hypothetical ORFs are assigned with potential functions by using similarity search with BLAST program. Re-annotation of the genome will benefit related researches on this hyperthermophilic crenarchaeon. Also, the re-annotation procedure could be taken as a reference for other archaeal genomes. Details of the revised annotation are freely available at http://cobi.uestc.edu.cn/resource/paero/

Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation

The specific binding of ligands is the first step of gene expression or translation regulation by riboswitches. However, understanding the mechanism of the specific binding is still difficult because the tertiary structures of the riboswitch aptamers are available almost only for ligand-bound state at present. In this paper we hope to give some insights into this problem through the studies of the role of ligand-aptamer interaction in the structural organization of add A-riboswitch aptamer, based on the crystal structure of the ligand-bound aptamer. We use all-atom molecular dynamics to simulate the behaviors of the aptamer in ligand-bound, free and mutated states by Amber force field. The results show that the correct paring of the ligand adenine with the nucleotide U74 in the binding pocket is crucial to stabilizing the conformations of the ligand-bound aptamer, especially the helix P1 connecting the expression platform. Our results also suggest that both the nucleotide U74 and U51 may be the key sites of the ligand recognition but the former has much higher probability as the initial docking site. This is in agreement with previous experimental results.

From lipid transport to oxygenation of aromatic compounds: evolution within the Bet v1-like superfamily

In absence of significant sequence similarity, remote homology between proteins can be confused with analogy and in such a case, shared ancestry can be inferred in light of certain unique and common features. In the present study, to understand the evolutionary origin of catalytic domain of large subunit of ring-hydroxylating oxygenases (RHOs), belonging to the Bet v1-like superfamily, structure-based phylogenies have been derived from structural alignment of representative proteins of the superfamily. A careful inspection of the structural relatedness of RHOs with the rest of the families showed closest similarity between RHO catalytic domain and PA1206-like protein. In addition, phylogenetic relationship of the Rieske domain of the large subunit of RHOs with functionally and structurally similar proteins has also been elucidated so as to postulate the most possible events leading to the genesis of the large subunit of RHOs.

Screening from the world's largest TCM database against H1N1 virus

The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.

Weighted relative entropy for alignment-free sequence comparison based on Markov model

In this paper, we introduce a probabilistic measure for computing the similarity between two biological sequences without alignment. The computation of the similarity measure is based on the Kullback-Leibler divergence of two constructed Markov models. We firstly validate the method on clustering nine chromosomes from three species. Secondly, we give the result of similarity search based on our new method. We lastly apply the measure to the construction of phylogenetic tree of 48 HEV genome sequences. Our results indicate that the weighted relative entropy is an efficient and powerful alignment-free measure for the analysis of sequences in the genomic scale.

Genome-wide identification and evolutionary analysis of Arabidopsis sm genes family

Sm proteins are members of a family of small proteins that are widespread in biosphere and found associated with RNA metabolism. To date, to our knowledge, only Arabidopsis SAD1 gene has been studied functionally in plant. In this study, 42 Sm genes are identified through comprehensive analysis in Arabidopsis. And a complete overview of this gene family is presented, including the gene structures, phylogeny, chromosome locations, selection pressure and expression. The results reveal that gene duplication contributes to the expansion of the Sm gene family in Arabidopsis genome, diverse expression patterns suggest their functional differentiation and divergence analysis indicates purifying selection as a key role in evolution. Our comparative genomics analysis of Sm genes will provide the first step towards the future experimental research on determining the functions of these genes.

An efficient binomial model-based measure for sequence comparison and its application

Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.