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SEA-PHAGES Course: Faculty Favorites (19)
These papers have been recommended by SEA-PHAGES faculty who have used primary literature to drive the learning of the science behind the SEA-PHAGES protocols and curriculum. These citations can be used for In Situ and/or In Silico portions of the SEA-PHAGES course, and for journal clubs, background reading, or assigned content. Some of these citations are specific to mycobacteriophages and some more broadly applicable.
Mycobacteriophage Bxb1 integrates into the Mycobacterium smegmatis groEL1 gene.
Molecular microbiology
Kim AI et al, 2003
A Phage Integration and Immunity Paper.

Recommendation: This paper provides details of phage integration and how it is investigated. Figure 1 shows the sequences of the attP and attB sites for phage Bxb1 (subcluster A1). The methods section specifies PCR primers that bind near these sites and identify integrated phage DNA, when used on DNA isolated from lysogens.

This is used in the in silico portion of the course, as background for understanding phage integration, and by students whose research projects focused on determining whether a new A1 phage used the same attachment site as previously published.
Dr. Karen Klyczek
Transcriptional regulation and immunity in mycobacteriophage Bxb1.
Molecular microbiology
Jain S, Hatfull GF, 2000
A Phage Integration and Immunity Paper.

Recommendation: This paper is helpful for understanding the function of repressors. It describes the repressor proteins of Bxb1 (A1) and L5 (A2). It compares the sequences of these proteins and also the binding sites (stoperators). It also provides wet lab support for the size of the repressor protein (170 aa for Bxb1), which is helpful for annotation.

This is used in the in silico portion of the course.
Dr. Karen Klyczek
Genome organization and characterization of mycobacteriophage Bxb1.
Molecular microbiology
Mediavilla J et al, 2000
A Phage Integration and Immunity Paper.

Recommendation: This paper provides background information about the mechanisms of immunity and how it is investigated in the lab. It shows the genome locations of stoperator (repressor binding) sequences in Bxb1 (A1) and L5 (A2). It also describes immunity testing with A1 and A2 phages.

This is used in the in silico portion of the course.
Dr. Karen Klyczek
The evolution of the tape measure protein: units, duplications and losses.
BMC Bioinformatics
Belcaid M, Bergeron A, Poisson G., 2011
This is used in In Silico and discusses tape measure protein in the context of broader evolution.
Dr. Shallee Page
Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution
PLoSOne
Pope WH et al, 2011
A Phage Integration and Immunity Paper.

Recommendation: This paper illustrates several ways that new phages can be investigated experimentally, and examples of interesting findings. For example, it characterizes new cluster A phages and the relationships between immunity mechanisms subcluster A1-A4 phages, including repressor sequences, stoperator sequences, immunity testing (Table 6 and Figure 6).

This is used in the in silico portion of the course.
Dr. Karen Klyczek
Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4
PLoS One
Pope WH, Ferreira CM, Jacobs-Sera D, et al, 2011
We use this for a required journal club at the beginning of the In Silico semester. It works well because the students can understand most of the figures easily. It gets them thinking about some of the analysis they are about to do, including comparative genome analysis in Phamerator.
Dr. Julie Stanton
The phage-host arms race: shaping the evolution of microbes.
Bioessays.
Stern A, Sorek R., 2011
Used in In Silico. Required Content! This is an excellent article!
Dr. John Hatherill
Inactivation of mycobacteriophage D29 using ferrous ammonium sulphate as a tool for the detection of viable Mycobacterium smegmatis and M. tuberculosis.
Research in microbiology
McNerney R et al, 1998
I chose the paper because many of our pre-med students are interested in how phages can be used as diagnostic tools. Also, the experimental design is fairly old-school and easy to understand. After I gave a brief intro to the paper, the students worked in groups and answered questions about each figure/table (What is the question being addressed? What approach did the authors take to address the question? What were the results? How did the authors interpret the results? and Do you agree with their interpretation?)
Dr. Anne Scherer
DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics.
Molecular microbiology
Hatfull GF, Sarkis GJ, 1993
This is used in both In Situ and In Silico portions of the course as required reading. It is also used to introduce students to the primary literature on a relevant topic. This primary research article reports on the very first sequenced mycobacteriophage genome (L5) and although nearly 20 years old, it serves as a wonderful introduction to the world of mycobacteriophage genomes. The paper describes the major L5 genomic features including predicted genes and protein functions, genome structure and organization, and codon usage. It provides several excellent opportunities for students to read and evaluate different types of experimental data and scientific arguments.
Dr. Joseph Stukey
Conserved translational frameshift in dsDNA bacteriophage tail assembly genes
Mol Cell
Xu J, Hendrix RW, and Duda RL, 2004
We always have students use this for Journal Club toward the beginning of the in silico semester. Our students have successfully identified this frameshift in every genome we have sequenced so far, based on their knowledge from this paper. This really is a favorite paper of ours and we never skip it. - Dr. Sue Carson and Dr. Eric Miller, North Carolina State University
Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns
Genes Dev.
Belle, A., M. Landthaler and D. A. Shub. , 2002
We have used this successfully in Journal Club in the in silico portion of the course to start discussions on phage evolution and endonuclease activity. – Dr. Sue Carson and Dr. Eric Miller, North Carolina State University
The phage-host arms race: shaping the evolution of microbes.
Bioessays.
Stern A, Sorek R., 2011
This is used in In Silico and provides a great discussion about coevolution with phages and genetic exchange with hosts.
Dr. Shallee Page
Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction
Molecular Microbiology
Malys N, Nivinskas R., 2009
We have used this successfully in Journal Club in the in silico portion of the course to start discussions. The paper not only solidified what they know about RBS, but shows an “exception to the rule” which is nice to bring out. -Sue Carson and Eric Miller, North Carolina State University
Length determination in bacteriophage lambda tails
Cell
Katsura I, Hendrix RW., 1984
This is used in In Silico and provides a good discussion about size concordance of tail gene.
Dr. Shallee Page
The evolution of the tape measure protein: units, duplications and losses.
BMC Bioinformatics
Belcaid M, Bergeron A, Poisson G., 2011
This is used in In Silico and discusses tape measure protein in the context of broader evolution.
Dr. Shallee Page
In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil.
Gene
Henry M et al, 2010
This is used in In Silico and is a nice example of thorough annotation and analysis of a phage.
Dr. Shallee Page
Bacteriophages can treat and prevent Pseudomonas aeruginosa lung infections
The Journal of Infectious Diseases
Debarbieux L, Leduc D, Maura D, Morello E, Criscuolo A, Gros, 2010
This paper makes a great journal discussion toward the beginning of the in situ semester. It is very easy to understand and fairly low-tech, so students can understand it while they are starting to learn the structure of what a paper is like. It also draws students in because they can envision a “purpose” for phage—especially the pre-med students. -Sue Carson and Eric Miller, North Carolina State University
Tail length determination in bacteriophage T4
Virology
Abuladze NK, Gingery M, Tsai J, Eiserling FA., 1994
We have used this successfully in Journal Club in both semesters of the course in different years. We usually either do it as the last paper in the in situ semester, or the first of the in silico semester because it starts to allow the students to see the link between what they observe phenotypically and what they find in the genome annotations. -Sue Carson and Eric Miller, North Carolina State University
General nature of the genetic code for proteins
Nature
CRICK FH, BARNETT L, BRENNER S, WATTS-TOBIN RJ, 1961
Used in In Silico. Of course, classic paper!
Dr. Shallee Page