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Moraes LE, Blow MJ, Hawley ER, Piao H, Kuo R, Chiniquy J, Shapiro N, Woyke T, Fadel JG, Hess M. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. AMB Express 2017; 7:42. [PMID: 28211005 PMCID: PMC5313495 DOI: 10.1186/s13568-017-0338-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 01/13/2023] Open
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 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.
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Affiliation(s)
- Luis E. Moraes
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Matthew J. Blow
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hailan Piao
- Washington State University, Richland, WA 99354 USA
| | - Rita Kuo
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jennifer Chiniquy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - James G. Fadel
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
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Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M. Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics 2014; 18 Pt B:97-9. [PMID: 24958360 DOI: 10.1016/j.margen.2014.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 06/10/2014] [Accepted: 06/10/2014] [Indexed: 11/16/2022]
Abstract
The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel.
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Affiliation(s)
| | - Stephanie A Malfatti
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, CA, USA
| | | | | | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Foster
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Janet R Jansson
- DOE Joint Genome Institute, Walnut Creek, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jack A Gilbert
- Argonne National Laboratory, Lemont, IL, USA; University of Chicago, Chicago, IL, USA
| | - Susannah Green Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Matthias Hess
- Washington State University, Richland, WA, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA; Pacific Northwest National Laboratory, Chemical & Biological Process Development Group, Richland, WA, USA; Environmental Molecular Sciences Laboratory, Richland, WA, USA.
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Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M. Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng 2014; 111:1550-65. [PMID: 24728961 DOI: 10.1002/bit.25250] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/21/2014] [Accepted: 03/24/2014] [Indexed: 11/06/2022]
Abstract
Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.
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Affiliation(s)
- Hailan Piao
- School of Molecular Biosciences, Washington State University, Richland, Washington, 99352; Pacific Northwest National Laboratory, Richland, Washington
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Hawley ER, Piao H, Scott NM, Malfatti S, Pagani I, Huntemann M, Chen A, Glavina Del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD, Hess M. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 2014; 9:1259-74. [PMID: 25197496 PMCID: PMC4149020 DOI: 10.4056/sigs.5029016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders – and their metabolic capabilities – may be fundamental to the ecology of the SBC oil seep.
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Affiliation(s)
- Erik R Hawley
- Washington State University Tri-Cities, Richland, WA, USA
| | - Hailan Piao
- Washington State University Tri-Cities, Richland, WA, USA
| | | | - Stephanie Malfatti
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, CA, USA
| | | | | | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Brian Foster
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Janet Jansson
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Susannah Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jack A Gilbert
- Argonne National Laboratory, Lemont, IL, USA ; University of Chicago, Chicago, IL, USA
| | | | - Matthias Hess
- Washington State University Tri-Cities, Richland, WA, USA ; DOE Joint Genome Institute, Walnut Creek, CA, USA ; Washington State University, Pullman, WA, USA ; Pacific Northwest National Laboratory, Chemical & Biological Process Development Group, Richland, WA, USA ; Environmental Molecular Sciences Laboratory, Richland, WA, USA
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