Annotated Bibliography
Sailasya Gundlapudi and Deeksha Jain
3/18/2015
BNFO
Sailasya Gundlapudi
http://www.sciencedirect.com/science/article/pii/B9780123946218000157
Cluster C currently contains nine phages divided into two subclusters, C1 and C2; C2
contains just a single phage, Myrna. All form plaques that are not completely clear, but
also do not form stable lysogens, and their genomes do not encode any recognizable
features of temperate phages. In general, the eight Cluster C1 phages are very similar to
each other, while Myrna differs in a variety of ways. The C1 genomes are all relatively
long but similarly sized (153.7–156.1 kbp) and Myrna is substantially larger (165.6 kbp),
the largest of all the sequenced mycobacteriophage genomes. All of the Cluster C phages
have myoviral morphologies with 80-nm-diameter isometric heads and modest length (85
nm) contractile tails. Cluster C genomes are circularly permuted and terminally
redundant, although some (such as Bxz1) are unusual in that there is a long run of G-C
residues in the genome through which sequencing reactions typically fail (Pedulla et al.,
2003). The left end of Bxz1 is arbitrarily designated as being the first unique base
position after the G-string, and the other Cluster C phage genomes are represented and
numbered accordingly.
The genome organization of the Cluster C representative Bxz1 is shown in Figure 6. It
differs from all other mycobacteriophages in that few of the virion structure and assembly
genes have been defined and it is not obvious that they are organized syntenically with
respect to the genomes of Siphoviridae. However, Bxz1 gp124 and gp125 are similar to
major structural proteins of mycobacteriophage I3 (Ramesh and Gopinathan, 1994), and
gp129 is a putative tapemeasure protein, located immediately downstream of two genes
(127 and 128) predicted to be expressed via a programmed translational frameshift ( Fig.
6). Bxz1 gp135 and gp143 have similarity to other mycobacteriophage minor tail
proteins, gp133 has features suggesting it is a plausible minor tail protein, and gp137 is
related to Baseplate J proteins. Thus the region encoding genes 124–143 likely
corresponds to a set of genes involved in tail structure and assembly; we note that Bxz1
gp114 has similarities to some other mycobacteriophage tail proteins ( Fig. 6). The
location of the putative major capsid subunit is unclear, although gp112 has similarity to
phage head decoration proteins
Cluster C, as they mentioned previously in the paper, is of the family myoviridae.
You can see a putative tapemeasure protein (the salmon colored protein after the Tail assembly
chaperones) in this figure.
http://onlinelibrary.wiley.com/doi/10.1111/mmi.12918/full
"The non-contractile tailed siphophages comprise the largest group of phages
(Ackermann, 2007). For a siphophage to productively infect a new bacterial cell, it must
inject its genome through the multilayered cell envelope. The process by which this
occurs is not well understood. In a Gram-negative bacterial cell, the phage genome must
pass through the outer membrane, periplasmic space, peptidoglycan layer and inner
membrane to gain entry to the bacterial cytoplasm where replication can begin. This
process begins with the recognition of a receptor on the cell surface, such as
lipopolysaccharide or an outer membrane porin. Studies with phage λ have revealed that
the outer membrane protein LamB acts as the phage receptor, but the bacterial inner
membrane PtsM complex also plays a role in the infection process (Scandella and Arber,
1976). Other phages have been shown to depend on the presence of different proteins in
the cell envelope.
The phage tail tape measure protein (TMP) has also been implicated in genome injection.
In vitro studies with phage λ revealed that the presence of LamB in liposomes resulted in
the TMP extruding from the tail and associating with the liposome (Roessner and Ihler,
1984). This process allowed ions, but not proteins, to traverse the membrane (Roessner
and Ihler, 1986). These data suggested that the TMP forms a channel though the host cell
membrane that can be used for phage genome entry. Cryo-electron tomography studies of
the E. coli podophage T7 (Hu et al., 2013) and siphophage T5 (Bohm et al., 2001)
revealed channel-like structures emanating from these phages through the bacterial cell
envelope, providing in vivo support for this model. The mechanism(s) by which phage
proteins form this channel and interact with host proteins to mediate genome entry are
unclear."
http://www.sciencedirect.com/science/article/pii/S0022283613004786
"The identifiable strong conservation of gene order appears to be limited to the gpVgpG/gpGT-gpH region across a diverse set of phages [22]. This suggests that these four
proteins' function might be closely linked together and that they may evolve as a unit.
This is consistent with our results that show that the four proteins' functions are related,
with gpGT providing a bridge between major tail protein gpV and tape measure protein
gpH. Our results also provide a rational explanation for the broad conservation of
frameshifting among dsDNA tailed phages. That is, it appears that both the production of
two proteins sharing the same N-terminal sequence and keeping the two proteins in a
fixed ratio are very important. We incorporated our results in the assembly pathway
shown in Fig. 7. A major difference from the assembly pathways proposed earlier is that
we think gpG, gpGT, gpH, and possibly gpV form a subassembly in the assembly
pathway. A small amount of gpGT is incorporated into the complex between gpG and
gpH. The C-terminus of gpH is probably used to bind to the initiator [17], and gpGT
together with other factors in the initiator (e.g., gpL, gpM) induces gpV to polymerize
around the tape measure protein. When the tail reaches the length specified by the tape
measure protein, it will stop and be capped by gpU. The detailed picture of how gpG,
gpGT, gpV, and gpH interact with each other to form the complex structure is not known.
How gpG and gpGT are excluded in the final structure and how gpH is cleaved also
remain unanswered. Those questions cannot be answered until we have a more detailed
structural and biochemical characterization of the tail and tail assembly intermediates."
Four proteins gpV, gpG, gpGT, and gpH are linked together and may have evolved together and
deal with tail assembly (this includes the tape measure protein, gpH). These four proteins might
form a subassembly in the assembly pathway. GpGT gets inbetween gpG and gpH (tapemeasure)
proteins. The C-terminus of gpH (tapemeasure) binds to the initiator an gpGT (which is in the
initiator) makes gpV polymerize around gpH (tape measure protein). Finally, when the desired
tail length is achieved (as dictated by gpH) gpU caps it so it does not exceed it. This is extremely
important for our research project as it shows the protein pathways by which the tapemeasure
protein interacts with other proteins in order to regulate tail length.
http://www.sciencedirect.com/science/article/pii/S0042682284711287
"This report identifies a protein that regulates tail length in bacteriophage T4. Earlier
work (Duda et al., 1990) suggested that the gene 29 protein could be involved in T4 tail
length determination as a "template" or "tape-measure", similar to that proposed for the
gene H protein in bacteriophage λ. We have altered the length of a recombinant gene 29
by constructing deletions and duplications in different parts of the gene. Each of these
constructs was incorporated into the high-level expression vector, pET-11d. Seven
plasmids with different lengths of gene 29 were made and used in complementation
studies. We have found that the length of the tail can be decreased by deleting the Cterminal part of gene 29 or increased by forming duplications in different parts of this
gene, and that the length of the tail can be proportional to the size of the engineered
protein. Unlike phage λ, plasmids with deletions in the middle of gene 29 or from the Nterminal end produced correspondingly smaller but inactive gene 29 protein and no viable
phage were formed. Our results show that alterations in the length of gene 29 protein
proportionately alters tail length, and argue strongly for a scheme in which 29 protein is a
ruler or template that determines tail length during tail assembly."
This paper looked at the putative tapemeasure protein in a phage called T4, a myoviridae
bacteriophage. Previous research showed that the Gene 29 Protein could be the tapemeasure
protein in this phage. 7 plasmids were made from parts they took from gene 29 in order to see if
tail length could be altered by manipulating the gene 29 protein in these plasmids. By deleting
the C-terminal of gene 29, they were able to make the tail length shorter. Tail length was also
made longer by duplicating parts of the gene and inserting them in the places in the gene.
However, sometimes changes made within the protein within the plasmids would result in a nonviable phage, which occured when parts of the N-terminal end or gene 29 were deleted, which
resulted in a smaller gene 29 protein and no viable phage. Gene 29 protein in T4 is probably a
tape measure protein that regulates tail length during tail assembly. The results of this study are
important as usually when a protein is altered, the protein becomes non-viable and loses its
ability to function; however, in this case, when the protein was altered in a specific way it was
still able to function and aid in assembling a tail (albeit of a different length). This is something
to look into further throughout the course of this project.
Deeksha Jain
http://www.sciencedirect.com/science/article/pii/S1369527406000038
“In bacteriophage λ, the length of the tail (150 nm) is controlled by a 92 kDa protein
encoded by gene H (Figure 1a). In-frame deletions and duplications in gene H lead to
proportionately shorter or longer tails, and the length of the tail is proportional to the size
of the protein, suggesting that the product of gene H (gpH) acts as a molecular ruler or a
‘tape-measure protein’ (TMP) [1 and 6]. gpH is also part of the complex which nucleates
polymerization of gpV, the tail subunit protein. This model proposes that gpV
polymerizes around gpH, which thus, acts both as a scaffold and a ruler. When the
growing tail reaches the amino-terminal domain of the ruler, the end becomes naked,
polymerization pauses, and this enables the growth-terminating protein gpU to lock the
tail at the correct size and to connect it to a head [7].”
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185693/#b26-viruses-03-00172
“The length of Sipho- and Myoviridae tails is determined by a tape-measure or ruler
protein, also found in cellular complexes such as an injectesome (also called a type III
secretion system) and the hook of flagellum [26]. The presence of the ruler protein was
first identified in bacteriophage lambda and later in bacteriophage T4 and T5 [167–169].
Presumably, the ruler protein is stretched the entire length of the tail and acts as a
scaffold for the polymerization of the tail tube [170]……. The copy number of ruler
proteins per phage is unknown, but for the type III secretion system it was determined
that only one ruler protein is present per complex [171].”
http://www.biomedcentral.com/1471-2164/13/331
“A total of 11 bacteriophage tail structural protein homologs were identified; among
these were the bacteriophage tape measure protein, which functions in determination of
bacteriophage tail length (homologs 1 (NP_463477), 2 (YP_239811) and 11 (P44236),
respectively). Homolog 9 (YP_398561) is a transglycosylase related to the bacteriophage
tape measure protein, TP901 family. The bacteriophage protein gp37, homologous to the
long tail fiber receptor recognizing protein [homolog 3 (P03744)], allows the specific
attachment of the bacteriophage to the bacteria and specifies the host range of the
bacteriophage.”
http://mmbr.asm.org/content/75/3/423.full
“The three Caudovirales families. From left to right are the Myoviridae(T4), the
Podoviridae (P22), and the Siphoviridae (p2). (B) Schematic representation of the typical
genome organization within theSiphoviridae tail morphogenesis module (this
organization is also observed for several myophages with some adaptations). Trp, tail
terminator; MTP, major tail protein; C and C*, tail chaperones; TMP, tape measure
protein; Dit, distal tail protein; gp27-like/Tal (tail-associated lysozyme or tail fiber), the
presence of a C-terminal domain depends on the phage considered; P1 and P2,
baseplate/tip peripheral proteins (their number varies among phages).”
http://www.sciencedirect.com/science/article/pii/S0022283613004786
"Bacteriophage λ makes two proteins with overlapping amino acid sequences that are
essential for tail assembly. These two proteins, gpG and gpGT, are related by a
programmed translational frameshift that is conserved among diverse phages and
functions in λ to ensure that gpG and the frameshift product gpGT are made in a molar
ratio of approximately 30:1. Although both proteins are required and must be present in
the correct ratio for assembly of functional tails, neither is present in mature tails. During
λ tail assembly, major tail protein gpV polymerizes to form a long tube whose length is
controlled by the tape measure protein gpH. We show that the “G” domains of gpG and
gpGT bind to all or parts of tail length tape measure protein gpH and that the “T” domain
of gpGT binds to major tail shaft subunit gpV, and present a model for how gpG and
gpGT chaperone gpH and direct the polymerization of gpV to form a tail of the correct
length."
http://onlinelibrary.wiley.com/doi/10.1111/j.13652958.2006.05473.x/abstract;jsessionid=349FA57CD100281C174FC49367294823.f01t04?syste
mMessage=Wiley+Online+Library+will+be+disrupted+on+7th+March+from+10%3A0013%3A00+GMT+%2805%3A0008%3A00+EST%29+for+essential+maintenance.++Apologies+for+the+inconvenience
"Within these phage genomes the tape measure protein (tmp) gene can be readily
identified due to the well-established relationship between the length of the gene and the
length of the phage tail – because these phages typically have long tails, the tmp gene is
usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain
small motifs with sequence similarity to host proteins. One of these motifs (motif 1)
corresponds to the Rpf proteins that have lysozyme activity and function to stimulate
growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of
unknown function, although some of the related proteins of the host are predicted to be
involved in cell wall catabolism. We show here that motif 3-containing proteins have
peptidoglycan-hydrolysing activity and that while this activity is not required for phage
viability, it facilitates efficient infection and DNA injection into stationary phase cells.
Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a
selective disadvantage that results from changes in peptidoglycan in non-growing cells."