Special Issue "Focus Update in Biomolecules"

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 December 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Jürg Bähler
Department of Genetics, Evolution & Environment and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
Website: http://www.bahlerlab.info
E-Mail: j.bahler@ucl.ac.uk
Phone: +44 2031 081602
Fax: +44 2076 797096
Interests: gene regulation; genomics; transcriptomics; next-generation sequencing; non-coding RNAs; genome evolution; fission yeast; oxidative stress response; cellular quiescence and ageing

Special Issue Information

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Published Papers (6 papers)

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Displaying article 1-6
p. 315-353
by ,  and
Biomolecules 2014, 4(1), 315-353; doi:10.3390/biom4010315
Received: 24 December 2013; in revised form: 11 February 2014 / Accepted: 27 February 2014 / Published: 14 March 2014
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(This article belongs to the Special Issue Focus Update in Biomolecules)
p. 217-234
by  and
Biomolecules 2014, 4(1), 217-234; doi:10.3390/biom4010217
Received: 30 December 2013; in revised form: 24 January 2014 / Accepted: 4 February 2014 / Published: 18 February 2014
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(This article belongs to the Special Issue Focus Update in Biomolecules)
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p. 140-159
by , , , ,  and
Biomolecules 2014, 4(1), 140-159; doi:10.3390/biom4010140
Received: 25 December 2013; in revised form: 21 January 2014 / Accepted: 23 January 2014 / Published: 10 February 2014
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(This article belongs to the Special Issue Focus Update in Biomolecules)
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p. 76-100
by ,  and
Biomolecules 2014, 4(1), 76-100; doi:10.3390/biom4010076
Received: 25 November 2013; in revised form: 18 December 2013 / Accepted: 27 December 2013 / Published: 7 January 2014
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(This article belongs to the Special Issue Focus Update in Biomolecules)
p. 943-966
by  and
Biomolecules 2013, 3(4), 943-966; doi:10.3390/biom3040943
Received: 28 September 2013; in revised form: 1 November 2013 / Accepted: 2 November 2013 / Published: 11 November 2013
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(This article belongs to the Special Issue Focus Update in Biomolecules)
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p. 905-922
by ,  and
Biomolecules 2013, 3(4), 905-922; doi:10.3390/biom3040905
Received: 22 August 2013; in revised form: 23 October 2013 / Accepted: 29 October 2013 / Published: 6 November 2013
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Title:
Complex Formation between Holliday Junction (HJ) Recombinatorial Intermediate Structures and the Yeast Orthologs of Bloom’s Syndrome Helicase/Topoisomerase
Author
: Ferez S. Nallaseth
Affiliation
: Center for Advanced Biotechnology and Medicine/Rutgers University, Piscataway, NJ, USA; E-Mail: ferez.nallaseth@gmail.com
Abstract:
Mutant BLM the human ortholog of the prototypical  E.coli RecQ helicase family forms heterocomplexes with a number of tumor suppressor and DNA repair proteins associated with elevated recombination frequencies, genomic instability and cancer. The yeast (S. cerevisiae) ortholog of this human heteromer is Sgs1 helicase (BLM), Top3 topoisomerase (TOPO IIIα) and Rmi1 (hRMI1) trimer. Using EMSAs and a ‘Pull Down Assay’ we have shown that among 10 DNA  structures tested, the Rmi1 monomer preferentially binds to HJ and pseudo-replication forks (pRF). The contributions of each subunit of the yeast Sgs1 / Top3 / Rmi1 trimer to complex formation with non-branch migratable HJs was assayed with a gentle biotinylated DNA / Streptavidin-Sepharose bead ‘Pull Down Assay’. In the presence of Rmi1 the binding of Top3 to HJs is not only significantly elevated it also acquires a preference for HJs. Once bound to HJs, Top3 displaces Rmi1 from these complexes. Both interactions are identical to those of TOPO IIIα with hRMI1 on dHJs. Finally, low level binding to HJs by Sgs1 Helicase N-terminus domains (that interact with Top3) is stimulated by the Rmi1 / Top3 dimer but inhibited by either monomer alone. However, as DNA unwinding by helicases is a pre-requisite for replication the subsequent requirement for Top3 / Rmi1 in retaining preloaded Sgs1 on HJ by-products of replication seems redundant. One explanation is a distinction between DNA helicase and dHJ dissolution / resolution functions of Sgs1 that is imposed by DNA structure. This requires unloading and reloading of Sgs1 from dHJ at stalled forks. Consistent with this interpretation, the affinity for HJ of the Rmi1 moiety of the heteromer is ~6x higher than it’s affinity for pRF as measured by EMSAs. These results may identify pre-requisites for fork progression through double dHJs.

Type of Paper: Review
Title: Structure and Function of the Bi-Directional Bacterial Flagellar Motor
Authors: Yusuke Morimoto and Tohru Minamino *
Affiliation: Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; * E-Mail: tohru@fbs.osaka-u.ac.jp (T.M.)
Abstract: The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical screw. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of four proteins, FliF, FliG, FliM, and FliN, and a dozen stators consisting of two integral membrane proteins, MotA and MotB. FliG, FliM, and FliN act as a switch complex, enabling the motor to spin in both counterclockwise and clockwise directions. The stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel to torque generation. Highly conserved charged residues at the stator-rotor interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will focus on the structure and function of the proton-driven bacterial flagellar motor.

Type of Paper: Review
Title:
Control of cell differentiation by mitochondria, typically evidenced in Dictyostelium development
Authors:
Yasuo Maeda1,* and Junji Chida 2
Affiliations:
1Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan; E-mail: kjygy352@ybb.ne.jp (Y.M.); 2Division of Molecular Neurobiology, Institute for Enzyme Research, The University of Tokushima, Kuramoto-cho, Tokushima 770-8503, Japan; E-Mail: jchida@tokushima-u.ac.jp (J.C.)
Abstract:
In eukaryotic cells, mitochondria are self-reproducing organelles with their own DNA and they play a central role in adenosine triphosphate (ATP) synthesis by respiration. Increasing evidence indicates that mitochondria also have critical and multiple functions in the initiation of cell differentiation, cell-type determination, cell movement, and pattern formation. This has been most strikingly realized in development of the cellular slime mold Dictyostelium. For example, the expression of the mitochondrial ribosomal protein S4 (mt-rps4) gene is required for the initial differentiation. The Dictyostelium homologue (Dd-TRAP1) of TRAP-1 (tumor necrosis receptor-associated protein 1), a mitochondrial molecular chaperone belonging to the Hsp90 family, allows the prompt transition of cells from growth to differentiation through a novel prestarvation factor (PSF-3) in growth medium. Moreover, a cell-type-specific organelle named a prespore-specific vacuole (PSV) is constructed by mitochondrial transformation with the help of the Golgi complex. Mitochondria are also closely involved in a variety of cellular activities including CN-resistant respiration and apoptosis. These mitochondrial functions are reviewed in this article, with special emphasis on the regulation of Dictyostelium development.
Key
words: Differentiation, Mitochondria, Mitochondrial ribosomal protein S4 (mt-RPS4), tumor necrosis receptor-associated protein 1 (TRAP-1), CN-resistant respiration, Prespore-specific vacuole (PSV), Dictyostelium

Last update: 23 September 2013

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