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Title: The essential gene set of a photosynthetic organism

Abstract

Synechococcus elongatus PCC 7942 is a model organism used for studying photosynthesis and the circadian clock, and it is being developed for the production of fuel, industrial chemicals, and pharmaceuticals. To identify a comprehensive set of genes and intergenic regions that impacts fitness in S. elongatus , we created a pooled library of ∼250,000 transposon mutants and used sequencing to identify the insertion locations. By analyzing the distribution and survival of these mutants, we identified 718 of the organism’s 2,723 genes as essential for survival under laboratory conditions. The validity of the essential gene set is supported by its tight overlap with well-conserved genes and its enrichment for core biological processes. The differences noted between our dataset and these predictors of essentiality, however, have led to surprising biological insights. One such finding is that genes in a large portion of the TCA cycle are dispensable, suggesting that S. elongatus does not require a cyclic TCA process. Furthermore, the density of the transposon mutant library enabled individual and global statements about the essentiality of noncoding RNAs, regulatory elements, and other intergenic regions. In this way, a group I intron located in tRNA Leu , which has been used extensively for phylogeneticmore » studies, was shown here to be essential for the survival of S. elongatus . Our survey of essentiality for every locus in the S. elongatus genome serves as a powerful resource for understanding the organism’s physiology and defines the essential gene set required for the growth of a photosynthetic organism.« less

Authors:
 [1];  [2];  [2];  [1];  [1];  [1];  [1];  [3];  [1];  [1]
  1. Univ. of California, San Diego, La Jolla, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
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:
1235172
Alternate Identifier(s):
OSTI ID: 1378675
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 112; Journal Issue: 48; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; RB-TnSeq; transposon mutagenesis; Tn-seq; cyanobacteria; photosynthesis

Citation Formats

Rubin, Benjamin E., Wetmore, Kelly M., Price, Morgan N., Diamond, Spencer, Shultzaberger, Ryan K., Lowe, Laura C., Curtin, Genevieve, Arkin, Adam P., Deutschbauer, Adam, and Golden, Susan S. The essential gene set of a photosynthetic organism. United States: N. p., 2015. Web. doi:10.1073/pnas.1519220112.
Rubin, Benjamin E., Wetmore, Kelly M., Price, Morgan N., Diamond, Spencer, Shultzaberger, Ryan K., Lowe, Laura C., Curtin, Genevieve, Arkin, Adam P., Deutschbauer, Adam, & Golden, Susan S. The essential gene set of a photosynthetic organism. United States. doi:10.1073/pnas.1519220112.
Rubin, Benjamin E., Wetmore, Kelly M., Price, Morgan N., Diamond, Spencer, Shultzaberger, Ryan K., Lowe, Laura C., Curtin, Genevieve, Arkin, Adam P., Deutschbauer, Adam, and Golden, Susan S. Tue . "The essential gene set of a photosynthetic organism". United States. doi:10.1073/pnas.1519220112.
@article{osti_1235172,
title = {The essential gene set of a photosynthetic organism},
author = {Rubin, Benjamin E. and Wetmore, Kelly M. and Price, Morgan N. and Diamond, Spencer and Shultzaberger, Ryan K. and Lowe, Laura C. and Curtin, Genevieve and Arkin, Adam P. and Deutschbauer, Adam and Golden, Susan S.},
abstractNote = {Synechococcus elongatus PCC 7942 is a model organism used for studying photosynthesis and the circadian clock, and it is being developed for the production of fuel, industrial chemicals, and pharmaceuticals. To identify a comprehensive set of genes and intergenic regions that impacts fitness in S. elongatus , we created a pooled library of ∼250,000 transposon mutants and used sequencing to identify the insertion locations. By analyzing the distribution and survival of these mutants, we identified 718 of the organism’s 2,723 genes as essential for survival under laboratory conditions. The validity of the essential gene set is supported by its tight overlap with well-conserved genes and its enrichment for core biological processes. The differences noted between our dataset and these predictors of essentiality, however, have led to surprising biological insights. One such finding is that genes in a large portion of the TCA cycle are dispensable, suggesting that S. elongatus does not require a cyclic TCA process. Furthermore, the density of the transposon mutant library enabled individual and global statements about the essentiality of noncoding RNAs, regulatory elements, and other intergenic regions. In this way, a group I intron located in tRNA Leu , which has been used extensively for phylogenetic studies, was shown here to be essential for the survival of S. elongatus . Our survey of essentiality for every locus in the S. elongatus genome serves as a powerful resource for understanding the organism’s physiology and defines the essential gene set required for the growth of a photosynthetic organism.},
doi = {10.1073/pnas.1519220112},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 48,
volume = 112,
place = {United States},
year = {2015},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1073/pnas.1519220112

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Cited by: 25 works
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    Works referencing / citing this record:

    The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
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    Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastoris
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    Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973
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