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Special Issue "Structural and Functional Biology of Hypothetical Proteins in Marine Life"

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A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (30 June 2010)

Special Issue Editor

Guest Editor
Prof. Dr. Joseph David Ng

Department of Biological Science and Laboratory for Structural Biology, University of Alabama in Huntsville, AL, 301 Sparkman Dr., Huntsville, AL 35899, USA
Website | E-Mail
Fax: +1 256 824 3204
Interests: structural and functional biology related to marine proteins; X-ray and neutron crystallography; biomolecular engineering

Special Issue Information

Dear Colleagues,

Hypothetical proteins (HPs) are predicted gene products that have no identifiable function assigned to them. They comprise 10-60% of recognized open reading frames (ORFs) in annotated genomes, including ~50% of human ORFs. These unknown gene products may be unique to the organism or orthologous to proteins in other organisms. Many genes identified in sequenced genomes of both marine and terrain organisms have a significant portion of their predicted gene products to be "Hypothetical" and may serve as conserved factors critical for cellular survival among all life forms. These types of proteins play critical roles both inside and outside of the cell in catalysis, regulation, transport, storage, scaffolding, pathogenesis, signaling defense, growth and development. In this respect HPs are completely unexplored targets for potential therapeutic drugs. This special issue of Marine Drugs will focus on the specific question of "What is the functional significance of the thousands of genes that encode for hypothetical proteins unique or common among genomes representing marine microorganism, plants and animals?" Great efforts will be directed towards extremophiles or symbiotic microorganisms. The collection of reviews and studies in this issue will encompass work related to (1) discovering novel or conserved HPs in the targeted genomes using bioinformatics; (2) identifying the cellular location and developmental time of HP mRNA expression using techniques such as PCR-based analyses, proteomics mass spectrometry, polysome-bound mRNA profiling and high throughput microarray analysis; and (3) conducting structural studies using the tools of NMR spectroscopy and X-ray crystallography. This issue aims to provide a broader understanding of inter-species interactions, providing a comprehensive overview of signal transduction proteins, transcription factors, classically and non–classically secreted proteins involved in various pathogenic, non-pathogenic, symbiotic and saprophytic life styles of marine life and their relationship to those found on land.

Prof. Dr. Joseph D. Ng
Guest Editor

Keywords

  • hypothetical proteins
  • functional genomics
  • X-ray crystallography
  • NMR spectroscopy
  • extremophiles
  • symbiotic microorganisms
  • extremophilic gene, structure and function
  • extremophilic drug discovery and design

Published Papers (2 papers)

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Research

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Open AccessArticle Cloning and Comparative Studies of Seaweed Trehalose-6-Phosphate Synthase Genes
Mar. Drugs 2010, 8(7), 2065-2079; doi:10.3390/md8072065
Received: 17 May 2010 / Revised: 4 June 2010 / Accepted: 30 June 2010 / Published: 6 July 2010
Cited by 4 | PDF Full-text (224 KB) | HTML Full-text | XML Full-text
Abstract
The full-length cDNA sequence (3219 base pairs) of the trehalose-6-phosphate synthase gene of Porphyra yezoensis (PyTPS) was isolated byRACE-PCR and deposited in GenBank (NCBI) with the accession number AY729671. PyTPS encodes a protein of 908 amino acids before a stop codon,
[...] Read more.
The full-length cDNA sequence (3219 base pairs) of the trehalose-6-phosphate synthase gene of Porphyra yezoensis (PyTPS) was isolated byRACE-PCR and deposited in GenBank (NCBI) with the accession number AY729671. PyTPS encodes a protein of 908 amino acids before a stop codon, and has a calculated molecular mass of 101,591 Daltons. The PyTPS protein consists of a TPS domain in the N-terminus and a putative TPP domain at the C-terminus. Homology alignment for PyTPS and the TPS proteins from bacteria, yeast and higher plants indicated that the most closely related sequences to PyTPS were those from higher plants (OsTPS and AtTPS5), whereas the most distant sequence to PyTPS was from bacteria (EcOtsAB). Based on the identified sequence of the PyTPS gene, PCR primers were designed and used to amplify the TPS genes from nine other seaweed species. Sequences of the nine obtained TPS genes were deposited in GenBank (NCBI). All 10 TPS genes encoded peptides of 908 amino acids and the sequences were highly conserved both in nucleotide composition (>94%) and in amino acid composition (>96%). Unlike the TPS genes from some other plants, there was no intron in any of the 10 isolated seaweed TPS genes. Full article

Review

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Open AccessReview Pharmacological Analyses of Protein Kinases Regulating Egg Maturation in Marine Nemertean Worms: A Review and Comparison with Mammalian Eggs
Mar. Drugs 2010, 8(8), 2417-2434; doi:10.3390/md8082417
Received: 21 June 2010 / Revised: 24 July 2010 / Accepted: 20 August 2010 / Published: 24 August 2010
Cited by 8 | PDF Full-text (379 KB) | HTML Full-text | XML Full-text
Abstract
For development to proceed normally, animal eggs must undergo a maturation process that ultimately depends on phosphorylations of key regulatory proteins. To analyze the kinases that mediate these phosphorylations, eggs of marine nemertean worms have been treated with pharmacological modulators of intracellular signaling
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For development to proceed normally, animal eggs must undergo a maturation process that ultimately depends on phosphorylations of key regulatory proteins. To analyze the kinases that mediate these phosphorylations, eggs of marine nemertean worms have been treated with pharmacological modulators of intracellular signaling pathways and subsequently probed with immunoblots employing phospho-specific antibodies. This article both reviews such analyses and compares them with those conducted on mammals, while focusing on how egg maturation in nemerteans is affected by signaling pathways involving cAMP, mitogen-activated protein kinases, Src-family kinases, protein kinase C isotypes, AMP-activated kinase, and the Cdc2 kinase of maturation-promoting factor. Full article

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