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Genus-specific, sRNA discovery in marine Synechococcus

Walworth, Nathan (2011) BIOP34 20102
Degree Projects in Biology
Abstract
Genus-specific, sRNA discovery in marine Synechococcus

The most ubiquitously distributed, picocyanobacteria, Synechococcus significantly contribute to global, oceanic primary productivity and are pivotal players in biogeochemical cycling. Because of the distribution and significant contribution of picocyanobacterial to global processes, there have been many studies on gene expression and their transcriptional factors. More recently, small (sRNA) or regulatory non-coding RNAs (ncRNAs) are being proven to contribute considerably to transcriptional control and subsequent environmental responses. sRNAs or ncRNAs are a heterogenous group of functional RNA molecules devoid of a protein coding function, which assist in the regulation of gene... (More)
Genus-specific, sRNA discovery in marine Synechococcus

The most ubiquitously distributed, picocyanobacteria, Synechococcus significantly contribute to global, oceanic primary productivity and are pivotal players in biogeochemical cycling. Because of the distribution and significant contribution of picocyanobacterial to global processes, there have been many studies on gene expression and their transcriptional factors. More recently, small (sRNA) or regulatory non-coding RNAs (ncRNAs) are being proven to contribute considerably to transcriptional control and subsequent environmental responses. sRNAs or ncRNAs are a heterogenous group of functional RNA molecules devoid of a protein coding function, which assist in the regulation of gene expression in response to fluctuating environmental conditions. Furthermore, it is of great interest to target the discovery and annotation of the vast group of unknown, ncRNAs in the marine Synechococcus, cellular system to try and identify exclusive, beneficial genetic elements. In this study I have adapted a general bio-computational pipeline for ncRNA discovery to identify sequences exclusive to marine Synechococcus by targeting conserved, intergenic regions based on their genomic locations, folding patterns, and similar sequence elements to previously defined ncRNA’s. Two putative sRNA’s were selected in our analysis, ss1 and ss2. ss1 is located adjacent to every copy of the critical photo-stress gene, psbA while also sharing similar sequence elements and secondary structure to the previously defined ncRNA, DsrA. Although unique to Synechococcus, ss1’s consensus structure with DsrA may suggest homologous functionality and monophyletic origin. ss2 resides in the operon containing RuBisCO, which has been horizontally transferred throughout bacterial evolution while also sharing similar sequence elements and secondary structure with the recently defined Yfr1, sRNA family. So although these putative sRNA’s are Synechococcus¬-specific, both share similar sequence elements and secondary structure to other taxa-specific ncRNA’s as described in other studies. This may suggest that although sRNA’s are specific to certain phyla potentially indicating selective advantage, ncRNA’s may also have specific, unique monophyletic origins that have undergone combinations of both divergent and concerted evolution contingent upon differential genomic localities and recombination events. sRNA genetic regulation is likely far more common than is generally known, which is reflected in the considerable challenges in characterizing consensus sequences, structures, functions, and location. Integrating sRNA’s into our basic understanding of transcriptional units is critical in characterizing genetic control and subsequent evolution.



Advisors: Karin Rengefors, Eric Webb, Bill Nelson
Master´s Degree Project in Molecular Ecology, 60 credits, 2011
Department of Biology, Lund University

Small, non-coding RNA’s in the Cyanobacterium, Synechcoccus

This study explores novel, small RNA’s that do not code for proteins but regulate genetic control in the ubiquitous, marine cyanobacterium Synechococcus. It is of much interest to study the genetic elements controlling both the biology and ecology of this organism because it is distributed in high abundance throughout the world and is a pivotal primary producer at the start of oceanic food chains, which subsequently controls much of our biogeochemical cycles (i.e. carbon, nitrogen, etc.). Synechococcus is one of the most ancient photosynthetic cells and its ecological success throughout evolution makes it an important subject of study in relations to its genes and the elements controlling them.
As a general pipeline, DNA is transcribed into RNA (gene) and then RNA is subsequently translated into protein. However, there are many intermediate steps going from DNA to RNA to protein. Environmental factors usually turn certain genes on or off, like a light switch. However, more recent studies have found that small genetic elements, small (sRNA) or non-coding RNA’s (ncRNA), act on the gene switch and can regulate the degree to which each gene is turned off or on. It is kind of like having a light switch that can make the light brighter or dimmer. So, not only are genes turned on or off, they can be turned on or off to a certain degree. This type of genetic control is not well described in cyanobacterium but if we want to understand how the environment affects genes, then we must characterize small, ncRNA’s.
In order to find my small RNA’s, I employed a comparative genomics screen. I took intergenic regions in different genomes of Synechococcus and computationally located certain regions that were conserved (the same) in all genomes. Based on their chemical properties, structures, and location in the genome, I was able to pick a few that seem to have regulatory function while sharing similar elements to previously defined sRNA’s. Lastly, I only chose sRNA’s that were specific to marine Synechococcus. Below is one of my sRNA’s.
In choosing sRNA’s specific to marine Synechococcus, I was identifying sRNA’s that have been specifically retained in this genus throughout evolution, which could indicate that Synechococcus needed these genetic sequences for survival. Very little studies thus far have identified genus specific sRNA’s. This was the first marine Synechococcus specific scan for sRNA’s controlling gene expression related to stress response mechanisms. Subsquently, I need to do some molecular biology lab protocols to verify my sequences do indeed exist and are contributing to genetic control and ecological success.

Advisors: K Rengefors, E Webb, WC Nelson
Master´s Degree Project in Molecular Ecology, 60 credits. May 23rd, 2011
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Walworth, Nathan
supervisor
organization
course
BIOP34 20102
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
2174436
date added to LUP
2011-10-17 15:54:35
date last changed
2013-03-26 13:55:06
@misc{2174436,
  abstract     = {Genus-specific, sRNA discovery in marine Synechococcus

The most ubiquitously distributed, picocyanobacteria, Synechococcus significantly contribute to global, oceanic primary productivity and are pivotal players in biogeochemical cycling. Because of the distribution and significant contribution of picocyanobacterial to global processes, there have been many studies on gene expression and their transcriptional factors. More recently, small (sRNA) or regulatory non-coding RNAs (ncRNAs) are being proven to contribute considerably to transcriptional control and subsequent environmental responses. sRNAs or ncRNAs are a heterogenous group of functional RNA molecules devoid of a protein coding function, which assist in the regulation of gene expression in response to fluctuating environmental conditions. Furthermore, it is of great interest to target the discovery and annotation of the vast group of unknown, ncRNAs in the marine Synechococcus, cellular system to try and identify exclusive, beneficial genetic elements. In this study I have adapted a general bio-computational pipeline for ncRNA discovery to identify sequences exclusive to marine Synechococcus by targeting conserved, intergenic regions based on their genomic locations, folding patterns, and similar sequence elements to previously defined ncRNA’s. Two putative sRNA’s were selected in our analysis, ss1 and ss2. ss1 is located adjacent to every copy of the critical photo-stress gene, psbA while also sharing similar sequence elements and secondary structure to the previously defined ncRNA, DsrA. Although unique to Synechococcus, ss1’s consensus structure with DsrA may suggest homologous functionality and monophyletic origin. ss2 resides in the operon containing RuBisCO, which has been horizontally transferred throughout bacterial evolution while also sharing similar sequence elements and secondary structure with the recently defined Yfr1, sRNA family. So although these putative sRNA’s are Synechococcus¬-specific, both share similar sequence elements and secondary structure to other taxa-specific ncRNA’s as described in other studies. This may suggest that although sRNA’s are specific to certain phyla potentially indicating selective advantage, ncRNA’s may also have specific, unique monophyletic origins that have undergone combinations of both divergent and concerted evolution contingent upon differential genomic localities and recombination events. sRNA genetic regulation is likely far more common than is generally known, which is reflected in the considerable challenges in characterizing consensus sequences, structures, functions, and location. Integrating sRNA’s into our basic understanding of transcriptional units is critical in characterizing genetic control and subsequent evolution.



Advisors: Karin Rengefors, Eric Webb, Bill Nelson
Master´s Degree Project in Molecular Ecology, 60 credits, 2011
Department of Biology, Lund University

Small, non-coding RNA’s in the Cyanobacterium, Synechcoccus

This study explores novel, small RNA’s that do not code for proteins but regulate genetic control in the ubiquitous, marine cyanobacterium Synechococcus. It is of much interest to study the genetic elements controlling both the biology and ecology of this organism because it is distributed in high abundance throughout the world and is a pivotal primary producer at the start of oceanic food chains, which subsequently controls much of our biogeochemical cycles (i.e. carbon, nitrogen, etc.). Synechococcus is one of the most ancient photosynthetic cells and its ecological success throughout evolution makes it an important subject of study in relations to its genes and the elements controlling them.
As a general pipeline, DNA is transcribed into RNA (gene) and then RNA is subsequently translated into protein. However, there are many intermediate steps going from DNA to RNA to protein. Environmental factors usually turn certain genes on or off, like a light switch. However, more recent studies have found that small genetic elements, small (sRNA) or non-coding RNA’s (ncRNA), act on the gene switch and can regulate the degree to which each gene is turned off or on. It is kind of like having a light switch that can make the light brighter or dimmer. So, not only are genes turned on or off, they can be turned on or off to a certain degree. This type of genetic control is not well described in cyanobacterium but if we want to understand how the environment affects genes, then we must characterize small, ncRNA’s.
In order to find my small RNA’s, I employed a comparative genomics screen. I took intergenic regions in different genomes of Synechococcus and computationally located certain regions that were conserved (the same) in all genomes. Based on their chemical properties, structures, and location in the genome, I was able to pick a few that seem to have regulatory function while sharing similar elements to previously defined sRNA’s. Lastly, I only chose sRNA’s that were specific to marine Synechococcus. Below is one of my sRNA’s. 
In choosing sRNA’s specific to marine Synechococcus, I was identifying sRNA’s that have been specifically retained in this genus throughout evolution, which could indicate that Synechococcus needed these genetic sequences for survival. Very little studies thus far have identified genus specific sRNA’s. This was the first marine Synechococcus specific scan for sRNA’s controlling gene expression related to stress response mechanisms. Subsquently, I need to do some molecular biology lab protocols to verify my sequences do indeed exist and are contributing to genetic control and ecological success.

Advisors: K Rengefors, E Webb, WC Nelson
Master´s Degree Project in Molecular Ecology, 60 credits. May 23rd, 2011
Department of Biology, Lund University},
  author       = {Walworth, Nathan},
  language     = {eng},
  note         = {Student Paper},
  title        = {Genus-specific, sRNA discovery in marine Synechococcus},
  year         = {2011},
}