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Revealing the secrets of ‘known unknown’ genes in marine cyanobacteria
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Torcello-Requena, Alberto (2022) Revealing the secrets of ‘known unknown’ genes in marine cyanobacteria. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b3903275
Abstract
Marine picocyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant group of phototrophs on Earth. Despite their importance and being considered model organisms, the number of ‘known unknown’ genes in their genomes represents the majority of sequenced genes for both genera. The aim of this thesis was to begin to infer the function of a few of these ‘known unknown’ genes including in the phage that infect them. Initially, I obtained a bioinformatics framework of what we know of ‘known unknown’ genes in marine picocyanobacteria by collecting genomic data into a SQL database. Due to the sheer number of hypothetical genes found, a more pattern-oriented approach was required. Thus, the SQL database allowed us to formally query genomes and begin to formulate and answer questions regarding their function. Subsequently, to complement this database, a bioinformatics analysis of the viruses infecting marine picocyanobacteria (cyanophage) was made focusing particularly on auxiliary metabolic genes (AMG). To complement each of the bioinformatics chapters, subsequent experimental work focused on a specific ‘hypothetical’ protein either from the host (Psip1) and cyanophage. Psip1 was shown to be a novel high-affinity alkaline phosphatase, being found only in picocyanobacterial taxa inhabiting P-deplete oceanic regions and highly expressed in environmental metatranscriptomes. Conversely, I showed that a subset of a novel group of cyanophage S-PM2 genes specifically induced during infection of a P-deplete host were controlled by the Synechococcus host PhoB protein representing a new, albeit sub-optimal, mechanism to overcome P limitation during infection. This thesis thus demonstrates the opportunity and rewards for elucidating the function of ‘known’ unknown genes in marine microorganisms, not only providing new tools and knowledge for future applications, but also discerning the complex biology key to understanding the biogeochemical cycling of key elements in Earth’s largest biome the oceans.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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Library of Congress Subject Headings (LCSH): | Cyanobacteria -- Genetics, Marine bacteria, Bacterial genetics, Bioinformatics | ||||
Official Date: | September 2022 | ||||
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Institution: | University of Warwick | ||||
Theses Department: | School of Life Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Scanlan, David J. ; Chen, Yin ; Millard, Andrew ; Puxty, Richard John | ||||
Format of File: | |||||
Extent: | 213 leaves : colour illustrations, charts | ||||
Language: | eng |
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