Transcript Scenario 2 - people.vcu.edu

Scenario 2
Anotation: Gene of which something known
What follows is a simulation of an orf page in the proposed
graphical interface. The interface does not yet exist. As you go
through the simulation please consider what capabilities you
would want to serve your research and annotation interests.
A narrative to help you go through the simulation appears in a
red-bordered box, such as the one below.
To begin:
1. Click on Slide Show, (on the upper toolbar)
2. Click View Show
3. Click Continue button
Continue
Main Menu
Annotate
Options
History
Anabaena PCC 7120: alr1152
Replicon: Chromosome
Coordinates: 1356962 (start-ATG) -> 1357843 (stop)
Length = 293 amino acids
Human
A
Function: solitary Type II DNA methyltransferase (GGCC-specific)
Classification: Type II alpha (N4)
Experiment
Human
A
Activity:
Modification: N4-methylcytosine (inner cytosine of GGCC)
Protects against: HaeIII
In vivo activity: exists
Experiment
Experiment
Experiment
A
Expression: no data
Syny6803:sll1330: (click to expand)
Experiment
Strand: Direct
Gene name(s): dmtB, avaVIIM, dmnB
Mutant: Knockout loses GGCC methylation. Otherwise no known difference
from wild-type
Experiment
This is an example of an orf that has substantial human annotation.
Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003
The source of each assertion is given at the right. Press Continue .
Continue
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A
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Main Menu
Annotate
Options
History
Anabaena PCC 7120: alr1152
Replicon: Chromosome
Coordinates: 1356962 (start-ATG) -> 1357843 (stop)
Length = 293 amino acids
Human
A
Function: solitary Type II DNA methyltransferase (GGCC-specific)
Classification: Type II alpha (N4)
Experiment
Human
A
Activity:
Modification: N4-methylcytosine (inner cytosine of GGCC)
Protects against: HaeIII
In vivo activity: exists
Experiment
Experiment
Experiment
A
Expression: no data
Syny6803:sll1330: (click to expand)
Experiment
Strand: Direct
Gene name(s): dmtB, avaVIIM, dmnB
Mutant: Knockout loses GGCC methylation. Otherwise no known difference
from wild-type
Mouse over* to Experiment to the right of the Function
Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003
specification line to see where the assertion comes from.
*In real life, information will pop up when you mouse to an informative
position. In this simulation you’ll also need to click.
Experiment
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A
A
A
Main Menu
Annotate
Options
History
Anabaena PCC 7120: alr1152
Replicon: Chromosome
Coordinates: 1356962 (start-ATG) -> 1357843 (stop)
Length = 293 amino acids
Strand: Direct
Gene name(s): dmtB, avaVIIM, dmnB
Human
A
IDA: Matveyev et al
(2001)
Function: solitary Type II DNA methyltransferase (GGCC-specific)
Classification: Type II alpha (N4)
Experiment
Human
A
Activity:
Modification: N4-methylcytosine (inner cytosine of GGCC)
Protects against: HaeIII
In vivo activity: exists
Experiment
Experiment
Experiment
A
Expression: no data
Syny6803:sll1330: (click to expand)
Experiment
Mutant: Knockout loses GGCC methylation. Otherwise no known difference
from wild-type
IDA (Inferred from Direct Assay) is a standard
Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003
Gene Ontology Consortium descriptor, useful
for searching (see Scenario 3 for more).
Evidently there’s some hard evidence for the
assertion. To learn more, click on Experiment.
Experiment
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Back to Annotation page
Nucleic Acids Research (2001) 151:1491-1506
Full text article at
nar.oupjournals.orf
PubMed Central
access FREE full text articles
DNA methyltransferases of the cyanobacterium Anabaena PCC 7120
Andrey Matveyev, Kathryn T Young, Andrew Meng, and Jeff Elhai
Dept. of Biology, University of Richmond, Richmond VA USA
From the characterization of enzyme activities and the analysis of genomic sequences, the
complement of DNA methyltransferases (MTases) possessed by the cyanobacterium Anabaena
PCC 7120 has been deduced. Anabaena has nine DNA MTases. Four are associated with Type II
restriction enzymes (AvaI, AvaII, AvaIII and the newly recognized inactive AvaIV), and five are
not. Of the latter, four may be classified as solitary MTases, those whose function lies outside of
a restriction/modification system. The group is defined here based on biochemical and genetic
characteristics. The four solitary MTases, DmtA/M.AvaVI, DmtB/M.AvaVII, DmtC/M.AvaVIII
and DmtD/M.AvaIX, methylate at GATC, GGCC, CGATCG and rCCGGy, respectively. DmtB
methylates cytosines at the N4 position, but its sequence is more similar to N6-adenine MTases
than to cytosine-specific enzymes, indicating that it may have evolved from the former. The
solitary
MTases,are
appear
to betoofreferences
ancient origin
Annotations
linked
at within cyanobacteria, while the restriction
MTases appear to have arrived by recent horizontal transfer as did five now inactive Type I
PubMed and from there (sometimes) to
restriction systems. One MTase, M.AvaV, cannot reliably be classified as either a solitary or
full length
articles.
Click on button
restriction
MTase.
It is structurally
unusualtoand along with a few proteins of prokaryotic and
return
annotation
page.class of MTases distinct from all previously described.
eukaryotic
origintodefines
a structural
Main Menu
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History
Anabaena PCC 7120: alr1152
Replicon: Chromosome
Coordinates: 1356962 (start-ATG) -> 1357843 (stop)
Length = 293 amino acids
Human
A
Experiment
Human
A
Experiment
Experiment
Experiment
A
Strand: Direct
Gene name(s): dmtB, avaVIIM, dmnB
Function: solitary Type II DNA methyltransferase (GGCC-specific)
Classification: Type II alpha (N4)
Activity:
Modification:
(inner cytosine of GGCC)
The human N4-methylcytosine
annotations are propagated
Protects against:
HaeIII
throughout
all cyanobacterial
orthologs. Click
In vivo activity: exists
on Syny6803.C:sll0729 to see how this works.
Expression: no data
Syny6803:sll1330: (click to expand)
Mutant: Knockout loses GGCC methylation. Otherwise no known difference
from wild-type
Cyanobacterial orthologs: Syny6803.C:sll0729 NostPunc.352:003
A
A
A
Experiment
Experiment
A
Main Menu
Annotate
Options
History
Synechocystis PCC 6803: sll0729
Replicon: Chromosome
Coordinates: 3424667 (stop) <- 3425524 (start)
Length = 285 amino acids
System
Strand: Complement
Function: probable DNA methyltransferase
System
Anab7120.C:alr1152: solitary Type II DNA methyltransferase (GGCC-specific)
Experiment
Motifs:
pfm:MethyltransfD12: D12 class N6 adenine-specific DNA methyltransferase
ps:N6_MTASE: N-6 Adenine-specific DNA methylases signature.
System
System
Expression: (click to expand)
Mutant: none
Anab7120.C:alr1152: Knockout loses GGCC methylation. Otherwise no known
difference from wild-type
Experiment
Experiment
Cyanobacterial orthologs: Anab7120.C:alr1152 NostPunc.352:003
The annotation for the Anabaena gene appears automically on the
annotation page of its orthologs. This gives a hint to visitors to the
Synechocystis page that the system’s suggestion that Sll0729 is an
adenine methyltransferase may be [and is] wrong.
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End
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Scenario 2
Anotation: Gene of which something known
Summary
• Each assertion is linked to a justification.
• Justifying references are made available on-line.
• Annotations of an orf in one organism are propagated through
orthologs to other cyanobacteria.
The integration of annotation across all cyanobacterial genomes
makes possible the ideal of consideration of each gene by a
person expert in the field. This is achieved by dividing genes
vertically, by function, rather than horizontally, by species.