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Mycobacterium phage Optimus
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Detailed Information for Phage Optimus
Discovery Information
Isolation HostMycobacterium smegmatis mc²155
Found ByTaylor Mann
Year Found2010
Location FoundHolland, MI USA
Finding InstitutionHope College
ProgramScience Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science
From enriched soil sample?No
Isolation TemperatureNot entered
GPS Coordinates42.7895 N, 86.100953 W Map
Discovery NotesOptimus was found under approximately 8 cm of moist soil and decaying wood-chips. This soil was underneath a tree and about 2 feet away from a pedestrian sidewalk. The temperature was 24.4 degrees Celsius when collected.
Sequencing Information
Sequencing Complete?Yes
Date Sequencing CompletedJan 27, 2011
Genome length (bp)109270
Character of genome ends3' Sticky Overhang
Overhang Length4 bases
Overhang SequenceATCC
GC Content60.8%
Fasta file available?Yes: Download fasta file
Characterization
ClusterJ
Subcluster--
Cluster Life CycleTemperate
Other Cluster Members
Annotating InstitutionUnknown or unassigned
Annotation StatusIn GenBank
Plaque NotesAfter 24 hours of incubation at 37°C, the average plaque size was 1.325 mm. After 48 hours of incubation the average size varied depending on the density of phage. For phage with ample room to grow (less then approximately 350 plaque forming units), the average size was 4.76 mm. Plates that contained more then approximately 350 plaques were too difficult to measure because they ran into each other. After 72 hours of incubation with ample room to grow plaques grew to an average of 6.2 mm. After 72 hours of incubation Optimus ceased growth. The morphology of phage Optimus was very consistent once variations due to plaque density were accounted for. After 24 hours, a clear center was visible with a turbid area around that clear center, but the edges were not clearly defined. Furthermore, plaques near the edge of the plate had an oblong shape, resembling a comet tail. This comet tail always faced the edge of the plate while the clear center was closest to the middle of the plate. After 48 hours of incubation at 37°C not only was there a growth in plaque size, but there was also a more defined morphology. The edges of both the clear center and the turbid outer ring were more definite. Growth occurred in the turbid outer ring while the size of the clear center remained the same. The comet tail and clear center remain altered towards the edge and middle of the plate, respectively. Additionally, a higher concentration of bacteria surrounding the plaque was suggested by the lighter, more concentrated color. As the plaques grew in size, the relatively vague halo of bacteria concentration increases as suggested by the lighter coloration becoming more noticeable with the increase in plaque size. After 72 hours of incubation there was a slightly altered morphology, and an increase in bacteria surrounding the plaque as indicated by a lighter, more concentrated color. Under certain concentrations, around 250 plaques, the plaques formed another defined ring. The plaque morphology still contains a small clear center with a turbid ring and the comet tail effect; however, at 72 hours there were two additional rings on the outside of the original clear center and thick turbid ring. The first of these additional rings was more turbid then the second. In smaller plaque concentrations this last ring was faintly visible, but its edges were not as defined as those found in higher concentrations. Plates with more then approximately 300 plaques ran into each other after 72 hours so this morphology did not develop. After 72 hours of incubation, size and morphology of Optimus remain constant.
MorphotypeSiphoviridae
Number of Genes230
Number of tRNAs1
Has been Phamerated?Yes
Gene List

Click to View

Optimus_1

Optimus_2

Optimus_3

Optimus_4

Optimus_5

Optimus_6

Optimus_7
(terminase large subunit)

Optimus_8

Optimus_9
(portal protein)

Optimus_10
(capsid maturation protease)

Optimus_11
(major capsid protein)

Optimus_12

Optimus_13
(protein kinase catalytic domain protein)

Optimus_14
(methyltransferase domain protein)

Optimus_15
(glycosyltransferase domain protein)

Optimus_16

Optimus_17

Optimus_18

Optimus_19

Optimus_20

Optimus_21
(glucosyltransferase)

Optimus_22

Optimus_23
(head-to-tail adaptor)

Optimus_24
(head-to-tail stopper)

Optimus_25

Optimus_26
(tail terminator)

Optimus_27

Optimus_28

Optimus_29

Optimus_30
(tail assembly chaperone)

Optimus_31
(tail assembly chaperone)

Optimus_32
(tapemeasure protein)

Optimus_33
(endonuclease VII domain protein)

Optimus_34

Optimus_35
(minor tail protein)

Optimus_36

Optimus_37

Optimus_38

Optimus_39

Optimus_40

Optimus_41

Optimus_42

Optimus_43

Optimus_44

Optimus_45

Optimus_46

Optimus_47

Optimus_48

Optimus_49
(LamG domain protein)

Optimus_50

Optimus_51
(HNH endonuclease domain protein)

Optimus_52
(lysin A)

Optimus_53

Optimus_54
(lysin B)

Optimus_55

Optimus_56

Optimus_57
(NrdH)

Optimus_58

Optimus_59

Optimus_60

Optimus_61

Optimus_62

Optimus_63

Optimus_64
(Lsr2-like DNA-bridging protein)

Optimus_65

Optimus_66

Optimus_67

Optimus_68

Optimus_69

Optimus_70

Optimus_71

Optimus_72

Optimus_73

Optimus_74

Optimus_75

Optimus_76

Optimus_77

Optimus_78

Optimus_79
(integrase)

Optimus_80

Optimus_81
(endonuclease VII domain protein)

Optimus_82

Optimus_83

Optimus_84

Optimus_85

Optimus_86

Optimus_87

Optimus_88

Optimus_89

Optimus_90

Optimus_91

Optimus_92

Optimus_93

Optimus_94
(esterase-lipase domain protein)

Optimus_95

Optimus_96

Optimus_97

Optimus_98

Optimus_99

Optimus_100

Optimus_101

Optimus_102

Optimus_103

Optimus_104

Optimus_105

Optimus_106

Optimus_107

Optimus_108

Optimus_109

Optimus_110

Optimus_111

Optimus_112
(methyltransferase)

Optimus_113
(HNH endonuclease domain protein)

Optimus_114

Optimus_115

Optimus_116

Optimus_117

Optimus_118

Optimus_119
(polynucleotide kinase/phosphatase domain protein)

Optimus_120

Optimus_121
(endonuclease VII domain protein)

Optimus_122
(WhiB)

Optimus_123
(HTH DNA binding domain protein)

Optimus_124

Optimus_125

Optimus_126

Optimus_127

Optimus_128
(bifunctional DNA primase/polymerase)

Optimus_129

Optimus_130

Optimus_131

Optimus_132

Optimus_133

Optimus_134

Optimus_135
(HTH DNA-binding protein)

Optimus_136

Optimus_137

Optimus_138

Optimus_139

Optimus_140
(DnaB-like helicase)

Optimus_141

Optimus_142
(methylase)

Optimus_143

Optimus_144

Optimus_145

Optimus_146

Optimus_147

Optimus_148

Optimus_149
(RNA ligase)

Optimus_150
(Clp protease)

Optimus_151
(DnaQ-like exonuclease)

Optimus_152

Optimus_153

Optimus_154

Optimus_155

Optimus_156

Optimus_157

Optimus_158

Optimus_159

Optimus_160

Optimus_161

Optimus_162

Optimus_163

Optimus_164

Optimus_165

Optimus_166

Optimus_167

Optimus_168

Optimus_169

Optimus_170

Optimus_171

Optimus_172

Optimus_173

Optimus_174
(phosphoesterase)

Optimus_175

Optimus_176

Optimus_177

Optimus_178

Optimus_179

Optimus_180

Optimus_181

Optimus_183

Optimus_184

Optimus_185
(nucleotide hydrolase or transferase)

Optimus_186

Optimus_187

Optimus_188

Optimus_189

Optimus_190

Optimus_191

Optimus_192

Optimus_193
(FtsK-like protein)

Optimus_194

Optimus_195

Optimus_196

Optimus_197
(Ku protein)

Optimus_198

Optimus_199

Optimus_200

Optimus_201

Optimus_202

Optimus_203

Optimus_204

Optimus_205

Optimus_206

Optimus_207

Optimus_208

Optimus_209

Optimus_210

Optimus_211

Optimus_212

Optimus_213

Optimus_214

Optimus_215

Optimus_216

Optimus_217

Optimus_218

Optimus_219

Optimus_220

Optimus_221

Optimus_222

Optimus_223

Optimus_224

Optimus_225

Optimus_226

Optimus_227

Optimus_228

Optimus_229

Optimus_230

Optimus_231

Publication Info
Uploaded to GenBank?Yes
GenBank AccessionJF957059
Refseq NumberNone yet
Published in PaperPope, Bowman, Russell, et al 2015, eLIFE: Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity
Archiving Info
Archiving status Archived
Pitt Freezer Box# 2
Pitt Freezer Box Grid# E8
Available Files
Plaque PictureDownload
EM PictureDownload