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

Title: Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production

Abstract

Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without themore » need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.« less

Authors:
; ; ; ; ; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1344020
Alternate Identifier(s):
OSTI ID: 1379933
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
AMB Express
Additional Journal Information:
Journal Name: AMB Express Journal Volume: 7 Journal Issue: 1; Journal ID: ISSN 2191-0855
Publisher:
Springer Science + Business Media
Country of Publication:
Germany
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Nostoc punctiforme; cyanobacteria; carbon cycle; nitrogen cycle; natural product synthesis; single molecule real-time sequencing

Citation Formats

Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., and Hess, Matthias. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. Germany: N. p., 2017. Web. doi:10.1186/s13568-017-0338-9.
Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., & Hess, Matthias. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. Germany. doi:10.1186/s13568-017-0338-9.
Moraes, Luis E., Blow, Matthew J., Hawley, Erik R., Piao, Hailan, Kuo, Rita, Chiniquy, Jennifer, Shapiro, Nicole, Woyke, Tanja, Fadel, James G., and Hess, Matthias. Thu . "Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production". Germany. doi:10.1186/s13568-017-0338-9.
@article{osti_1344020,
title = {Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production},
author = {Moraes, Luis E. and Blow, Matthew J. and Hawley, Erik R. and Piao, Hailan and Kuo, Rita and Chiniquy, Jennifer and Shapiro, Nicole and Woyke, Tanja and Fadel, James G. and Hess, Matthias},
abstractNote = {Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy’s IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.},
doi = {10.1186/s13568-017-0338-9},
journal = {AMB Express},
number = 1,
volume = 7,
place = {Germany},
year = {2017},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s13568-017-0338-9

Save / Share:

Works referenced in this record:

Minimum Information about a Biosynthetic Gene cluster
journal, August 2015

  • Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin
  • Nature Chemical Biology, Vol. 11, Issue 9
  • DOI: 10.1038/nchembio.1890

Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event
journal, January 2013

  • Schirrmeister, B. E.; de Vos, J. M.; Antonelli, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 5
  • DOI: 10.1073/pnas.1209927110

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
journal, December 2007

  • Markowitz, V. M.; Szeto, E.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm846

Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil
journal, July 2016

  • Rice, Marlen C.; Norton, Jeanette M.; Valois, Frederica
  • Standards in Genomic Sciences, Vol. 11, Issue 1
  • DOI: 10.1186/s40793-016-0168-4

Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products
journal, April 2016

  • Gomez-Escribano, Juan; Alt, Silke; Bibb, Mervyn
  • Marine Drugs, Vol. 14, Issue 4
  • DOI: 10.3390/md14040078

Towards a Synthetic Chloroplast
journal, April 2011


An expanded evaluation of protein function prediction methods shows an improvement in accuracy
journal, September 2016


SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009


Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032
journal, September 2007


The expanding scope of DNA sequencing
journal, November 2012

  • Shendure, Jay; Aiden, Erez Lieberman
  • Nature Biotechnology, Vol. 30, Issue 11
  • DOI: 10.1038/nbt.2421

Genome sequence of the recombinant protein production host Pichia pastoris
journal, May 2009

  • De Schutter, Kristof; Lin, Yao-Cheng; Tiels, Petra
  • Nature Biotechnology, Vol. 27, Issue 6
  • DOI: 10.1038/nbt.1544

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013

  • Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2474

Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants
journal, November 2012


Cyanobacterial-based approaches to improving photosynthesis in plants
journal, October 2012

  • Zarzycki, Jan; Axen, Seth D.; Kinney, James N.
  • Journal of Experimental Botany, Vol. 64, Issue 3
  • DOI: 10.1093/jxb/ers294

A beginner's guide to eukaryotic genome annotation
journal, April 2012

  • Yandell, Mark; Ence, Daniel
  • Nature Reviews Genetics, Vol. 13, Issue 5
  • DOI: 10.1038/nrg3174

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Cyanobacterial biofuel production
journal, November 2012


Origin and Phylogeny of Chloroplasts Revealed by a Simple Correlation Analysis of Complete Genomes
journal, October 2003


Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

Cyanobacterial Cell Walls: News from an Unusual Prokaryotic Envelope
journal, March 2000


tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


The integrated microbial genomes system: an expanding comparative analysis resource
journal, October 2009

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp887

IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Curation of the genome annotation of Pichia pastoris ( Komagataella phaffii ) CBS7435 from gene level to protein function
journal, July 2016

  • Valli, Minoska; Tatto, Nadine E.; Peymann, Armin
  • FEMS Yeast Research, Vol. 16, Issue 6
  • DOI: 10.1093/femsyr/fow051

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015

  • Weber, Tilmann; Blin, Kai; Duddela, Srikanth
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv437

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

Tansley Review No. 107. Heterocyst and akinete differentiation in cyanobacteria
journal, October 1999


Regulation of Cellular Differentiation in Filamentous Cyanobacteria in Free-Living and Plant-Associated Symbiotic Growth States
journal, March 2002


Infernal 1.0: inference of RNA alignments
journal, March 2009


Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus
journal, November 2016

  • Cormier, Alexandre; Avia, Komlan; Sterck, Lieven
  • New Phytologist, Vol. 214, Issue 1
  • DOI: 10.1111/nph.14321

IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016

  • Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw929

Reducing assembly complexity of microbial genomes with single-molecule sequencing
journal, January 2013


Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation
journal, June 2016


The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

Direct detection of DNA methylation during single-molecule, real-time sequencing
journal, May 2010

  • Flusberg, Benjamin A.; Webster, Dale R.; Lee, Jessica H.
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1459