skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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}
}

Works referenced in this record:

Asymmetric Allosteric Signaling in Aspartate Transcarbamoylase
journal, March 2010

  • Mendes, Kimberly R.; Martinez, Jessica A.; Kantrowitz, Evan R.
  • ACS Chemical Biology, Vol. 5, Issue 5
  • DOI: 10.1021/cb9003207

Expression of the Cellulomonas fimi cellulase genes cex and cenA from the divergent tet promoters of transposon Tn10
journal, January 1990

  • Din, Neena; Beck, C. F.; Miller, R. C.
  • Archives of Microbiology, Vol. 153, Issue 2
  • DOI: 10.1007/BF00247809

Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation
journal, October 2013


CenC, a multidomain thermostable GH9 processive endoglucanase from Clostridium thermocellum: cloning, characterization and saccharification studies
journal, August 2015

  • Haq, Ikram ul; Akram, Fatima; Khan, Mahmood Ali
  • World Journal of Microbiology and Biotechnology, Vol. 31, Issue 11
  • DOI: 10.1007/s11274-015-1920-4

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

Differences in biomass degradation between newly isolated environmental strains of Clostridium thermocellum and heterogeneity in the size of the cellulosomal scaffoldin
journal, September 2015


The multidomain xylanase A of the hyperthermophilic bacterium Thermotoga neapolitana is extremely thermoresistant
journal, March 1996

  • Zverlov, V.; Piotukh, K.; Dakhova, O.
  • Applied Microbiology and Biotechnology, Vol. 45, Issue 1-2
  • DOI: 10.1007/s002530050678

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex
journal, February 2012

  • Brunecky, Roman; Alahuhta, Markus; Bomble, Yannick J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 3
  • DOI: 10.1107/S0907444912001680

Complex pectin metabolism by gut bacteria reveals novel catalytic functions
journal, March 2017

  • Ndeh, Didier; Rogowski, Artur; Cartmell, Alan
  • Nature, Vol. 544, Issue 7648
  • DOI: 10.1038/nature21725

The binding of Cellulomonas fimi endoglucanase C (CenC) to cellulose and Sephadex is mediated by the N-terminal repeats
journal, May 1992


Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: Genetic markers and characterization of cellulolytic potential
journal, July 2014

  • Koeck, Daniela E.; Zverlov, Vladimir V.; Liebl, Wolfgang
  • Systematic and Applied Microbiology, Vol. 37, Issue 5
  • DOI: 10.1016/j.syapm.2014.05.006

Evolutionary Implications of Bacterial Polyketide Synthases
journal, June 2005

  • Jenke-Kodama, Holger; Sandmann, Axel; Müller, Rolf
  • Molecular Biology and Evolution, Vol. 22, Issue 10
  • DOI: 10.1093/molbev/msi193

The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A
journal, September 2010

  • Alahuhta, Markus; Xu, Qi; Bomble, Yannick J.
  • Journal of Molecular Biology, Vol. 402, Issue 2
  • DOI: 10.1016/j.jmb.2010.07.028

Sequence analysis of the Clostridium cellulolyticum endoglucanase-A-encoding gene, celCCA
journal, December 1989


Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA
journal, November 2004

  • Kataeva, I. A.; Uversky, V. N.; Brewer, J. M.
  • Protein Engineering Design and Selection, Vol. 17, Issue 11
  • DOI: 10.1093/protein/gzh094

Duplicated Clostridium thermocellum cellobiohydrolase gene encoding cellulosomal subunits S3 and S5
journal, June 1999

  • Zverlov, V. V.; Velikodvorskaya, G. A.; Schwarz, W. H.
  • Applied Microbiology and Biotechnology, Vol. 51, Issue 6
  • DOI: 10.1007/s002530051473

Isolation of a Cellobiohydrolase of Clostridium thermocellum Capable of Degrading Natural Crystalline Substrates
journal, May 1993

  • Singh, R. N.; Akimenko, V. K.
  • Biochemical and Biophysical Research Communications, Vol. 192, Issue 3
  • DOI: 10.1006/bbrc.1993.1533

Cel9M, a New Family 9 Cellulase of the Clostridium cellulolyticum Cellulosome
journal, March 2002


Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass
journal, January 2013

  • Wilson, Charlotte M.; Rodriguez, Miguel; Johnson, Courtney M.
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-179

dbCAN: a web resource for automated carbohydrate-active enzyme annotation
journal, May 2012

  • Yin, Yanbin; Mao, Xizeng; Yang, Jincai
  • Nucleic Acids Research, Vol. 40, Issue W1
  • DOI: 10.1093/nar/gks479

Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis
journal, March 2012

  • Anbar, Michael; Gul, Ozgur; Lamed, Raphael
  • Applied and Environmental Microbiology, Vol. 78, Issue 9
  • DOI: 10.1128/AEM.07985-11

Modular enzymes
journal, January 2001

  • Khosla, Chaitan; Harbury, Pehr B.
  • Nature, Vol. 409, Issue 6817
  • DOI: 10.1038/35051723

Structural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from Clostridium thermocellum
journal, February 2004

  • Schubot, Florian D.; Kataeva, Irina A.; Chang, Jessie
  • Biochemistry, Vol. 43, Issue 5
  • DOI: 10.1021/bi030202i

Bacterial Cellulose Hydrolysis in Anaerobic Environmental Subsystems-Clostridium thermocellumandClostridium stercorarium, Thermophilic Plant-fiber Degraders
journal, March 2008

  • Zverlov, Vladimir V.; Schwarz, Wolfgang H.
  • Annals of the New York Academy of Sciences, Vol. 1125, Issue 1
  • DOI: 10.1196/annals.1419.008

Identification of endoxylanase XynE from Clostridium thermocellum as the first xylanase of glycoside hydrolase family GH141
journal, September 2017


Gene and protein nomenclature in public databases
journal, August 2006


A scheme for designating enzymes that hydrolyse the polysaccharides in the cell walls of plants
journal, March 1998


Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313
journal, April 2011

  • Feinberg, L.; Foden, J.; Barrett, T.
  • Journal of Bacteriology, Vol. 193, Issue 11, p. 2906-2907
  • DOI: 10.1128/JB.00322-11

Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2
journal, May 2012

  • Brown, S. D.; Lamed, R.; Morag, E.
  • Journal of Bacteriology, Vol. 194, Issue 12
  • DOI: 10.1128/JB.00473-12

Cloning and expression of Clostridium thermocellum genes coding for thermostable exoglucanases (cellobiohydrolases) in Escherichia coli cells
journal, June 1990

  • Tuka, K.; Zverlov, V. V.; Bumazkin, B. K.
  • Biochemical and Biophysical Research Communications, Vol. 169, Issue 3
  • DOI: 10.1016/0006-291X(90)92001-G