Document ID: EPA-HQ-OPP-2004-0135-0003
Agency: epa
Document Type: Supporting & Related Material
Title: 
Posted Date: 2004-04-28T04:00Z

1
UNITED
STATES
ENVIRONMENTAL
PROTECTION
AGENCY
WASHINGTON,
D.
C.
20460
APR
23
2004
OFFICE
OF
PREVENTION,
PESTICIDES
AND
TOXIC
SUBSTANCES
MEMORANDUM
SUBJECT:
Review
of
Supplemental
Data
on
the
Amino
Acid
Similarity
Comparison
for
Phosopho­
Mannose
Isomerase,
a
Plant­
Incorporated
Protectant
Inert
Ingredient.

TO:
Mike
Mendelsohn
Regulatory
Action
Leader
Microbial
Pesticides
Branch,
Biopesticides
and
Pollution
Prevention
Division
(
7511C)

FROM:
John
L.
Kough,
Ph.
D.,
Biologist
Microbial
Pesticides
Branch,
Biopesticides
and
Pollution
Prevention
Division
(
7511C)

ACTION
REQUESTED:
To
review
the
identified
proteins
shown
to
have
regions
of
significant
amino
acid
similarity
to
phospho­
mannose
isomerase
(
PMI).

CONCLUSION:
The
proteins
identified
as
having
significant
amino
acid
similarity
to
the
PMI
enzyme
are,
for
the
vast
majority,
enzymes
with
demonstrated
or
inferred
PMI
activity.
The
source
organisms
with
significant
similarity
to
PMI
were
identified
as
numerous
bacteria,
fungi,
plants,
insects,
and
mammals
as
well
as
a
nematode
and
protist.
This
wide
diversity
of
source
organisms
and
the
fact
that
PMI
is
involved
in
carbohydrate
metabolism
indicates
that
PMI
is
probably
a
housekeeping
enzyme
and
already
has
broad
expression
and
exposure.

DATA
REVIEW
RECORD
Inert
Ingredient:
Phospho­
Mannose
Isomerase
(
PMI)
2
Product
Name:
PMI
Company
Name:
Syngenta
Seeds,
Inc.
ID
No:
67979­
EUP­
G
Chemical
Number:
67979
Submission
Number:
S328476
DP
Barcode:
D292499
MRID
No:
462052­
01
BACKGROUND:
In
the
interest
of
utilizing
marker
proteins
in
plant
transformations
that
are
not
antibiotic
resistance
traits,
Syngenta
has
developed
a
selectable
marker
based
on
mannose
utilization.

DISCUSSION:
The
information
provided
indicates
that
all
the
proteins
with
similarities
to
the
Escherichia
coli
PMI
were
either
identified
PMI
enzymes,
putative
PMI
enzymes
or
hypothetical
open
reading
frames
for
PMI
proteins.
The
one
identified
protein
that
was
not
directly
named
a
PMI
was
identified
as
a
RNA
polymerase
sigma
factor.

The
source
organisms
with
significant
similarity
to
PMI
were
identified
as
numerous
bacteria,
fungi,
plants,
insects,
and
mammals
as
well
as
a
nematode
and
protist.
This
wide
diversity
of
source
organisms
and
the
fact
that
PMI
is
involved
in
carbohydrate
metabolism
indicates
that
PMI
is
probably
a
housekeeping
enzyme
and
already
has
broad
expression
and
exposure.

RECOMMENDATION:
There
is
a
reasonable
certainty
that
no
harm
will
result
from
the
aggregate
exposure
to
PMI
protein
as
a
selectable
marker
protein
and
an
inert
ingredient
for
PIPs.

SUMMARY
OF
DATA
SUBMITTED:
MRID
462052­
01
Supplemental
information
for
the
AA
similarity
comaprison.
CONCLUSION:
PMI
from
E.
coli
as
expressed
as
a
marker
protein
was
shown
to
have
significant
similarity
to
92
other
proteins
which
were
identified
as
other
PMI
enzymes,
putative
PMI
enzymes
or
hypothetical
open
reading
frames
for
PMIlike
proteins.
The
one
identified
protein
that
was
not
directly
named
a
PMI
was
identified
as
a
RNA
polymerase
sigma
factor.
CLASSIFICATION:
ACCEPTABLE.
3
DATA
EVALUATION
REPORT
Reviewed
by:
John
L.
Kough,
Ph.
D.,
Biologist,
BPPD
______________________________________________________________________________
STUDY
TYPE:
Supplemental
Information
on
Amino
Acid
Similarity
Comparison
MRID
NO:
462052­
01
CHEMICAL
NO:
67979
TEST
MATERIAL:
Phospho­
Mannose
Isomerase
STUDY
NO:
Report
No.
SSB­
101­
04
SPONSOR:
Syngenta
Seeds,
Inc.,
Research
Triangle
Park,
NC
TEST
FACILITY:
Syngenta
Seeds,
Inc.,
Research
Triangle
Park,
NC
TITLE
OF
REPORT:
Description
of
Phosphomannose
Isomerase
Protein
Homologues
Identified
in
Syngenta
Seeds
Biotechnology
Report
No.
SSB­
016­
03
AUTHOR:
Jennifer
Zawodny
STUDY
COMPLETED:
April
23,
2003
CONCLUSION:
PMI
from
E.
coli
as
expressed
as
a
marker
protein
was
shown
to
have
significant
similarity
to
92
other
proteins
which
were
identified
as
other
PMI
enzymes,
putative
PMI
enzymes
or
hypothetical
open
reading
frames
for
PMIlike
proteins.
The
one
identified
protein
that
was
not
directly
named
a
PMI
was
identified
as
a
RNA
polymerase
sigma
factor.
CLASSIFICATION:
ACCEPTABLE.
GLP
STATEMENT:
Not
GLP
compliant
however
raw
data
and
study
records
were
maintained.
_____________________________________________________________________________
STUDY
DESIGN
This
is
a
list
of
the
specific
proteins
identified
as
having
significant
degree
of
amino
acid
sequence
similarity
to
the
E.
coli
PMI
expressed
in
plants
as
a
selectable
marker
protein.

TEST
METHODS
The
amino
acid
sequence
of
the
E.
coli
PMI
as
expressed
in
plants
was
used
to
screened
using
the
BLASTP
program
against
other
proteins
found
in
the
GenBank
database.
The
cutoff
criterion
for
indicating
significant
similarity
was
an
E
value
of
0.42
or
less.

RESULTS
AND
DISCUSSION
The
92
proteins
identified
by
this
cutoff
were
either
identified
PMI
enzymes,
putative
PMI
enzymes
or
hypothetical
open
reading
frames
for
PMI­
like
proteins.
The
one
identified
protein
that
was
not
directly
named
a
PMI
was
identified
as
a
RNA
polymerase
sigma
factor.

The
source
of
the
various
PMI
proteins,
homologues
or
putative
open
reading
frames
ranged
from
enteric
bacteria
such
as
other
E.
coli
strains,
Shigella
and
Salmonella
(
with
E
values
of
0)
to
other
gram
negative
bacteria
like
Vibrio
and
Yersinia
(
with
E
values
very
close
to
0)
to
gram
positive
bacteria
such
Mycobacterium
and
Corynebacterium
to
actinomycetes
Streptomyces.
Also
included
in
the
matches
were
PMI
proteins
or
putative
proteins
from
organisms
like
yeasts,
fungi,
monkey,
man,
mouse,
plants,
nematode,
insects,
protists
and
numerous
other
bacterial
species.
This
wide
diversity
of
source
organisms
and
the
fact
that
PMI
is
involved
in
carbohydrate
metabolism
indicates
that
PMI
is
probably
a
housekeeping
enzyme
and
already
has
broad
expression
and
exposure.
While
the
listing
of
source
organisms
includes
numerous
bacterial
pathogens,
there
is
no
reason
to
believe
4
this
specific
enzyme
could
be
directly
linked
to
a
pathogenesis
factor.
Virulence
factors
tend
to
be
receptor
proteins,
membrane
active
enzymes
and
toxins
not
enzymes
involved
in
carbohydrate
metabolism
like
PMI.