The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli
Open accessAbstract
By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility. Thus, as the growth potential of the environment decreases, cells appear to devote progressively more energy on the mere possibility of improving conditions. This adaptation is not what would be predicated by classic regulatory models alone. We also observe an inverse correlation between gene activation and rRNA synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Significant differences in RNAP distribution in vivo, monitored using an RNAP-green fluorescent protein fusion, from energy-rich and energy-poor carbon source cultures support this hypothesis. Together, these findings represent the integration of both substrate-specific and global regulatory systems, and may be a bacterial approximation to metazoan risk-prone foraging behavior.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“As such, ALE studies highlight that duplications and large scale genomic variations, although they can lead to significant issues such as genomic instability [152], play a major role in e.g. yeast evolution; this is also indicated by data on wine yeasts, galactose utilization, comparative genomics and drug resistance [115,153-156].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [152]
Citations
Cites
Genetic regulatory mechanisms in the synthesis of proteins.
Jacob, F., & Monod, J. (1961) · Journal of Molecular Biology · doi:10.1016/s0022-2836(61)80072-7 · Cited by 5,300
Culture Medium for Enterobacteria
Neidhardt, F. C., Bloch, P. L., & Smith, D. F. (1974) · Journal of Bacteriology · doi:10.1128/jb.119.3.736-747.1974 · Cited by 2,903
Winer, J., Jung, C. K. S., Shackel, I., & Williams, P. M. (1999) · Analytical Biochemistry · doi:10.1006/abio.1999.4085 · Cited by 1,393
Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,008
Hengge‐Aronis, R. (2002) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.66.3.373-395.2002 · Cited by 931
TRANSCRIPTIONAL REGULATION BY cAMP AND ITS RECEPTOR PROTEIN
Kolb, A., Busby, S. J. W., BUC, H. C., Garges, S., & Adhya, S. L. (1993) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.62.070193.003533 · Cited by 848
Sperandio, V., Torres, A. G., & Kaper, J. B. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02803.x · Cited by 523
Lange, R., & Hengge‐Aronis, R. (1994) · Genes & Development · doi:10.1101/gad.8.13.1600 · Cited by 509
The languages of bacteriaPreprint
Schauder, S., & Bassler, B. L. (2001) · Genes & Development · doi:10.1101/gad.899601 · Cited by 462
Karp, P. D. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.56 · Cited by 453
Research works printed but not linked: 5
- Haralick, 1973, IEEE Trans. SMC, 3, 610
- Hengge-Aronis, 2002, J. Mol. Microbiol. Biotechnol., 4, 341
- Weyn, 2000, Anal. Quant. Cytol. Histol., 22, 373
- Cashel, 1996, 1, 1458
- Bremer, 1996, 2, 1553
Cited by
Sorted by citations
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
Görke, B., & Stülke, J. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1932 · Cited by 1,701
Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050008 · Cited by 1,563
Deutscher, J., Francke, C., & Postma, P. W. (2006) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00024-06 · Cited by 1,411
Adaptive laboratory evolution—Principles and applications for biotechnology
Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827
The global, ppGpp‐mediated stringent response to amino acid starvation in Escherichia coli
Traxler, M. F., Summers, S. M., Nguyen, H., Zacharia, V. M., Hightower, G. A., Smith, J. T., & Conway, T. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06229.x · Cited by 519
Metadata
- Authors
- Liu, M., Durfee, T., Cabrera, J. E., Zhao, K., Jin, D. J., & Blattner, F. R.
- Affiliations
- University of Wisconsin–Madison (US)
- National Institutes of Health (US)
- Corresponding author
- Blattner, Frederick R.
- ORCID
- Liu, Mingzhu
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2005-04
- Volume
- 280
- Issue
- 16
- Pages
- 15921-15927
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2081114359
- Cited by
- 209
- References
- 50
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 7 · 2023: 2 · 2022: 8 · 2021: 11 · 2020: 8 · 2019: 8 · 2018: 13 · 2017: 5 · 2016: 9 · 2015: 11 · 2014: 10 · 2013: 13 · 2012: 16
- FWCI
- 7.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM35682-17S1, R01GM035682)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Escherichia coli, global gene expression, ribosomal RNA synthesis, bacterial motility, energy allocation
- MeSH terms
- Alanine, Carbon, Computer Simulation, Escherichia coli, Glucose, Glycerol, Models, Biological, Proline, Promoter Regions, Genetic, RNA, Ribosomal, Transcription, Genetic, Up-Regulation, Acetic Acid, Succinic Acid, Gene Expression Profiling
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
