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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

  • Wolfgang H. Schwarz
  • Roman Brunecky
  • Jannis Broeker
  • Wolfgang Liebl
  • Vladimir V. Zverlov
Review

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.

Keywords

Gene annotation Gene naming Database handling Nomenclature Multimodular protein Gene sequencing Record tracking Non-catalytic modules 

Notes

Acknowledgements

A. Angelov, P. Kornberger, A. Ehrenreich and M. Mechelke are thanked for valuable comments. Financial support from the German Federal Ministry of Food and Agriculture (FNR Grant Number FKZ 22021715) for WHS, WL and VVZ, and from the European Commission (Collaborative FP7-KBBE Project Valor Plus, No. 613802) for JB is gratefully acknowledged.

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Authors and Affiliations

  1. 1.Department of Microbiology, TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
  2. 2.Biosciences CenterNational Renewable Energy LaboratoryGoldenUSA
  3. 3.Institute of Molecular GeneticsRussian Academy of ScienceMoscowRussia

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