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Predicted Light-Regulated Mechanisms in Freshwater Microbacteriaceae.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Predicted Light-Regulated Mechanisms in Freshwater Microbacteriaceae./
Author:	Hempel, Priscilla.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2024,
Description:	648 p.
Notes:	Source: Dissertations Abstracts International, Volume: 85-08, Section: B.
Contained By:	Dissertations Abstracts International85-08B.
Subject:	Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=30988133
ISBN:	9798381723281

Predicted Light-Regulated Mechanisms in Freshwater Microbacteriaceae.
Hempel, Priscilla.

Predicted Light-Regulated Mechanisms in Freshwater Microbacteriaceae. - Ann Arbor : ProQuest Dissertations & Theses, 2024 - 648 p.

Source: Dissertations Abstracts International, Volume: 85-08, Section: B.

Thesis (Ph.D.)--University of Delaware, 2024.

This item must not be sold to any third party vendors.

Light is an environmental cue and the most abundant source of energy on Earth. Many organisms in surface environments use and rely on light for energy, orientation with respect to time of day, location, and regulation of physiological processes. This includes microbes, which are the most abundant organisms on Earth. Microbes can sense and use light in a wide variety of ways. One way that microbes use light, is as a source of information and multiple light-sensing proteins that regulate physiological processes have been identified. However, the conversion of light to information and the subsequent cellular response(s) has only been characterized in a few species. Moreover, little is known about how bacteria use light as information that then enhances growth. While the use of light as a source of energy in photoautotrophs and photoheterotrophs has been highly characterized, the biological pathways involved in light-enhanced growth of bacteria lacking identifiable photosystems and functional rhodopsins had not been characterized. Sequence analyses, including genomic and transcriptomic, provide a comprehensive approach to the prediction of which metabolic processes are regulated by light. Insight into the bacterial use of light as a source of information to enhance growth expands our knowledge of bacterial sensing and provides insight into bacterial metabolism for future experiments. Identifying genes and biological functions present in bacterial species with light-enhanced growth, yet lacking identifiable photosystems and functional rhodopsins, is crucial for identifying potential light-capturing systems and predicting which proteins may be involved in the cellular response to light. Chapter 2 presents the genome sequences and annotations of three Actinobacteria species within the Microbacteriaceae family: Aurantimicrobium photophilum strain MWH-Mo1, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3 as well as the genome comparison of these three species and Rhodoluna lacicola strain MWH-Ta8. Previously, light-enhanced growth was observed in the two Aurantimicrobium species and R. lacicola, while Microbacterium sp. strain 10M-3C3 does not have light enhanced growth. Chapter 3 presents a pangenome analysis of 27 Microbacteriaceae, including R. lacicola, A. photophilum, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3. This was done to identify trends in the genetic differences between Microbacteriaceae isolated from different environments. Multiple predicted genes were found to be enriched in marine Microbacteriaceae and a few predicted genes were found to be enriched in terrestrial (freshwater and soil) Microbacteriaceae. These results contribute to our understanding of how Microbacteriaceae are specialized for their environment. Additionally, from the pangenome enrichment analysis, I was able to identify genes that are good candidates for further analysis to understand the light-enhanced growth phenotype in freshwater Microbacteriaceae.Lastly, the transcriptomes of two Microbacteriaceae with light-enhanced growth, R. lacicola and A. photophilum, are analyzed in Chapter 4. This work shows that although R. lacicola and A. photophilum have the same light-enhanced growth phenotype, which genes are light-regulated and their light-regulated expression patterns differed greatly. These results indicate that different mechanism(s) may be responsible for the increased growth rates in the light. Additionally, it suggests that R. lacicola and A. photophilum may have different signal transduction pathways and/or regulatory proteins that respond to light and darkness. The phylogenetic profiling and expression analyses within this work identified predicted regulatory proteins that are good candidates for future experiments testing the effects of light on physiological and biochemical properties of freshwater Actinobacteria, and identifying the cellular activities that correspond to light-induced transcriptional changes in these organisms.

ISBN: 9798381723281Subjects--Topical Terms:

583857
Bioinformatics.
Subjects--Index Terms:

Microbacteriaceae

Predicted Light-Regulated Mechanisms in Freshwater Microbacteriaceae.
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300 $a 648 p.
500 $a Source: Dissertations Abstracts International, Volume: 85-08, Section: B.
500 $a Advisor: Maresca, Julia A.
502 $a Thesis (Ph.D.)--University of Delaware, 2024.
506 $a This item must not be sold to any third party vendors.
520 $a Light is an environmental cue and the most abundant source of energy on Earth. Many organisms in surface environments use and rely on light for energy, orientation with respect to time of day, location, and regulation of physiological processes. This includes microbes, which are the most abundant organisms on Earth. Microbes can sense and use light in a wide variety of ways. One way that microbes use light, is as a source of information and multiple light-sensing proteins that regulate physiological processes have been identified. However, the conversion of light to information and the subsequent cellular response(s) has only been characterized in a few species. Moreover, little is known about how bacteria use light as information that then enhances growth. While the use of light as a source of energy in photoautotrophs and photoheterotrophs has been highly characterized, the biological pathways involved in light-enhanced growth of bacteria lacking identifiable photosystems and functional rhodopsins had not been characterized. Sequence analyses, including genomic and transcriptomic, provide a comprehensive approach to the prediction of which metabolic processes are regulated by light. Insight into the bacterial use of light as a source of information to enhance growth expands our knowledge of bacterial sensing and provides insight into bacterial metabolism for future experiments. Identifying genes and biological functions present in bacterial species with light-enhanced growth, yet lacking identifiable photosystems and functional rhodopsins, is crucial for identifying potential light-capturing systems and predicting which proteins may be involved in the cellular response to light. Chapter 2 presents the genome sequences and annotations of three Actinobacteria species within the Microbacteriaceae family: Aurantimicrobium photophilum strain MWH-Mo1, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3 as well as the genome comparison of these three species and Rhodoluna lacicola strain MWH-Ta8. Previously, light-enhanced growth was observed in the two Aurantimicrobium species and R. lacicola, while Microbacterium sp. strain 10M-3C3 does not have light enhanced growth. Chapter 3 presents a pangenome analysis of 27 Microbacteriaceae, including R. lacicola, A. photophilum, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3. This was done to identify trends in the genetic differences between Microbacteriaceae isolated from different environments. Multiple predicted genes were found to be enriched in marine Microbacteriaceae and a few predicted genes were found to be enriched in terrestrial (freshwater and soil) Microbacteriaceae. These results contribute to our understanding of how Microbacteriaceae are specialized for their environment. Additionally, from the pangenome enrichment analysis, I was able to identify genes that are good candidates for further analysis to understand the light-enhanced growth phenotype in freshwater Microbacteriaceae.Lastly, the transcriptomes of two Microbacteriaceae with light-enhanced growth, R. lacicola and A. photophilum, are analyzed in Chapter 4. This work shows that although R. lacicola and A. photophilum have the same light-enhanced growth phenotype, which genes are light-regulated and their light-regulated expression patterns differed greatly. These results indicate that different mechanism(s) may be responsible for the increased growth rates in the light. Additionally, it suggests that R. lacicola and A. photophilum may have different signal transduction pathways and/or regulatory proteins that respond to light and darkness. The phylogenetic profiling and expression analyses within this work identified predicted regulatory proteins that are good candidates for future experiments testing the effects of light on physiological and biochemical properties of freshwater Actinobacteria, and identifying the cellular activities that correspond to light-induced transcriptional changes in these organisms.
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653 $a Bacterial metabolism
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710 2 $a University of Delaware. $b Bioinformatics and Systems Biology. $3 1437838
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