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Title: Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum

Abstract

An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.

Authors:
 [1];  [2];  [2];  [2];  [3]
  1. National Renewable Energy Laboratory (NREL), Golden, CO (United States)
  2. Technical University of Munich
  3. Technical University of Munich; Russian Academy of Science
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1426635
Report Number(s):
NREL/JA-2700-71114
Journal ID: ISSN 0959-3993
DOE Contract Number:  
AC36-08GO28308
Resource Type:
Journal Article
Journal Name:
World Journal of Microbiology and Biotechnology
Additional Journal Information:
Journal Volume: 34; Journal Issue: 3; Journal ID: ISSN 0959-3993
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; gene annotation; gene naming; database handling; nomenclature; multimodular protein; gene sequencing; record tracking; non-catalytic modules

Citation Formats

Brunecky, Roman, Schwarz, Wolfgang H., Broeker, Jannis, Liebl, Wolfgang, and Zverlov, Vladimir V. Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum. United States: N. p., 2018. Web. doi:10.1007/s11274-018-2424-9.
Brunecky, Roman, Schwarz, Wolfgang H., Broeker, Jannis, Liebl, Wolfgang, & Zverlov, Vladimir V. Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum. United States. doi:10.1007/s11274-018-2424-9.
Brunecky, Roman, Schwarz, Wolfgang H., Broeker, Jannis, Liebl, Wolfgang, and Zverlov, Vladimir V. Mon . "Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum". United States. doi:10.1007/s11274-018-2424-9.
@article{osti_1426635,
title = {Handling Gene and Protein Names in the Age of Bioinformatics: The Special Challenge of Secreted Multimodular Bacterial Enzymes such as the cbhA/cbh9A Gene of Clostridium thermocellum},
author = {Brunecky, Roman and Schwarz, Wolfgang H. and Broeker, Jannis and Liebl, Wolfgang and Zverlov, Vladimir V.},
abstractNote = {An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.},
doi = {10.1007/s11274-018-2424-9},
journal = {World Journal of Microbiology and Biotechnology},
issn = {0959-3993},
number = 3,
volume = 34,
place = {United States},
year = {2018},
month = {2}
}