Dear Dr. Lerbs-Mache:

I am imposing on your time to hear your opinion about the nomenclature of
sigma factors from Arabidopsis.

Carl Price involved in the Commission on Plant Gene Nomenclature (CPGN)
consulted with me about the necessity of finding the consensus of
nomenclature of sigma factors before "The 6th International Congress of
Plant Molecular Biology" held in Quebec in last June. I then promised him
that I would survey all released nomenclatures of sigma factors from plants
and discuss among persons who proposed each nomenclature. I did not have
time to examine all released sequences with their nomenclatures.

Pal Maliga then by chance sent his note to Don Bourque who is the editor of
"Plant Molecular Biology Reporter", and it was forwarded to me through Carl
on July 18 as shown below.

> What prompted me to write this note is that I just saw a paper by Lori
> Allison describing maize plastid sigma factors ZmSig1, ZmSig2 and ZmSig3
> in Plant Physiol. 123:883-894, 2000. A paper by Tan and Troxler (PNAS
> 96:5316, 1999) is describing g a different set of maize plastid sigma
> factors as ZmSig1 and ZmSig2.

[deleted]

> Others mark their sigma factors as e.g.
> Arabidopsis At-SigA, etc.
>
> I suggest, that you invite the principal researchers on plastid sigma
> factors to prepare a contribution for the Plant Molecular Biology
> Reporter describing the unified nomenclature of plastid sigma factors.

I was unable to take care of this immediately, and now I am asking you
concerning the nomenclatures of Arabidopsis sigma factors. I will consult
with Bob Troxler and Lori Allison about the case of maize separately, and
put them together and report them to CPGN.

I have just realized that your interesting paper has been published in JBC
(275, 9215-9221, 2000) where you adopted the nomenclatures proposed by me.
However, early in July when I was still missing your JBC paper, I discussed
with Kan Tanaka and I agreed with him to employ common nomenclatures of
sigma factors of Arabidopsis. My personal proposal was in case of
Arabidopsis:

mine    Kan's    proposal
SIG2 = SigA -> SIG1
SIG1 = SigB -> SIG2
SIG3 = SigC -> SIG3
SIG4 = SigD -> SIG4
SIG5 = SigE -> SIG5
SIG6 = SigF -> SIG6

The new SIG1 is the most homologous to the gene encoding the sigma factor
first reported from tobacco, rice, mustard, and wheat, and highly expressed
in leaves.

However, the situation is now different from that I did not know
publication of your paper in JBC with my nomenclatures.

Two of my papers are going to be submitted. I have once changed my
nomenclatures to the new ones, but I now think this change makes readers
more confusion with publication of your paper. I have heard from Kan that
he is also submitting some papers with his own nomenclatures.

I would appreciate hearing your opinion and comments.

With best regards,

Hiro

Hirokazu Kobayashi
Laboratory of Plant Cell Technology
Graduate School of Nutritional and Environmental Sciences
UNIVERSITY OF SHIZUOKA
52-1 Yada, Shizuoka 422-8526, JAPAN
e-mail: hirokazu@smail.u-shizuoka-ken.ac.jp
http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/
phone: +81(Japan)-54-264-5582
fax: +81(Japan)-54-264-5584

Dear Hiro:

[deleted]

In regard to your earlier email, I have an idea for sigma factor
nomenclature. The easiest way to do it is to number sigma factors (1, 2, 3,
4, 5 and 6) on the basis of publication date. A disadvantage to this is that
the most important sigma factor (homologue of sigma 70 in E. coli that
transcribes housekeeping genes), if there is one, might not be given the
number "1" if it was the 3rd one to be published. An advantage my suggestion
is that it is perhaps most fair to scientists who discoverer sigma factors.
Another advantage may be that the story of sigma factors in chloroplasts
may turn out to be quite complex and may turn out to be quite different from
the story in E. coli. Therefore, the number of the sigma factor may be less
important overall.

[deleted]

I wish you great success and all the best.

With kindest regards.

Bob Troxler

Dear Dr. Kobayashi,

I returned just from vacation and I am sorry for the delay of
the reply. We have decided to use your nomenclature for sigma factors
for three different reasons: (1) because your PNAS paper was the
first and most important dealing with sequences of higher plant
plastid sigma factors. (2) our experiments show that only SIG1
(C-terminal sequence) can complement E. coli rpoD mutants, i. e. SIG1
is really a functional homologue to the E. coli principal sigma
factor, sigma-70. This is a good reason to call it number 1. (3) We have in
vivo results showing that SIG1 is an essential sigma factor
for plant development.

My suggestion would be to keep your nomenclature for
Arabidopsis. To facilitate the comparison of results obtained with
different plant species the Arabidopsis nomenclature should be
adopted to name sigma factors from other plant species according to
their sequence similarities with the Arabidopsis factors.

I hope that I could help you to solve the nomenclature
problem. If you have some new papers accepted - I would be glad to
receive reprints.

Sincerely,

Silva Lerbs-Mache

[deleted]

I have made a phylogenetic tree on the basis of comparison of regions
2.1 to 4.2 of sigma factors, which is hereto attached.

[deleted]

Although the properties of SIG1 designated by me and Lerbs-Mache most
resemble those of E. coli RpoD among SIG1, SIG2, and SIG3; SigE and
SigF are more closed to RpoD according to the attached phylogenetic
tree and in the expression profile observed at my lab. Therefore,
classification with their features is reasonable but is practically
difficult at the beginning of research.

Dear Hiro,

In your letter of 17 September you asked how people name members of
multigene families within a species.

At 1:35 AM 00.9.17, Hirokazu KOBAYASHI wrote:
> I consult with you about nomenclatures of submembers. In our present
> knowledge, plant sigma factors are classified into 6 groups, Sig1 to
> Sig6. I have not yet convinced of the best nomenclatures of
> submembers in tobacco and maize, which are amphidiploid and hybrid.
> Tanaka et al. designated "SigA1" and "SigA2" for sigma factors from
> tobacco, both of which belong to "Sig1" group in the proposed
> nomenclature. How do people name the submembers? The "SigA1" and
> "SigA2" are like allelic so that we may call them "Sig1-1" and
> "Sig1-2". However, if they are not allelic, the "Sig1-1" and
> "Sig1-2" are inadequate. I would appreciate hearing how people
> dissolve this kind of problem in the other genes.

The answer to your question is: many different ways!

The CPGN wrestled with this problem in our early discussions and came
up with the model of three fields. Individual genes would be identified
by:
the plant-wide gene family
the genus and species
a "member number," an integer based where possible on the
traditional names for the genes.

The three fields would be set off by semicolons.

To take your example, Tanaka's SigA1 and SigA2 genes in tobacco would
be designated:

NICta;Sig1;1
NICta;Sig1;2

A couple of caveates:

o Abbreviations for genus and species must be large enough to
accomodate all of the plant species subject to gene isolations. In the
current database there are 1622 plant genera that start with "A." I
don't know how many of those species start with "t," but if the
distribution were random, there would be 62 candidates for the
abbreviation "At"! We have adopted the Swiss-Prot model of five-letter
abbreviations: three for the genus and two for the species. But there
are already problems.

o It's important that the three fields be separated--not
attached. If we were to name individual genes AtSig64, NtSig62,
ZmSig61, a computerized search would have great difficulty pulling out
all of the members of Sig6.

Our recommendation is that you and your group recommend the names for
the gene families; we present your recommendations to the scientists
associated with the CPGN; and, when the recommendations are approved,
we turn to you for the assignment of member numbers.

Best,--

Carl--

C. A. Price
7521 Brava Street
La Costa, CA 92009-7504, USA
price@onemain.com
price@mbcl.rutgers.edu (can receive only)
ph: 1-760-942-6050fax: 1-760-479-0259

Dear Hiro,

thank you for kindly notifying me about the current status of the
plastid sigma nomenclature. I think you did a great job with putting
all the data together and you come up with a very balanced view.
I immediately agree to the new assignment, including the inverted
designation of Sig1/Sig2 (now matching SigA/SigB).

Sig1 (new nomenclature) indeed seems to be the most "Sig-70 like"
factor of Sig1, 2 and 3 (and perhaps of others as well, if one would
include more N-terminal regions than 2.1 in the tree?). In addition,
its transcript seems to be the most abundant one in a number of
species, which might be taken as another argument for its possible
role as "principal" plastid sigma factor.

Just as a suggestion: it would be helpful if in the future not every
author would have to bound to the "computer-readable" systematic
nomenclature. The identity sould be just made clear somewhere in
the paper, e.g. in the abbreviation list, like an enzyme EC number.

For me it is amazing to see the progress in the sigma field, and I
look forward to stay in contact with you and the other colleagues.

With kind regards,

Gerhard

Gerhard Link,
University of Bochum,
Plant Cell Physiology,
D-44780 Bochum,
Germany
Phone: +49-234-322-5495
Fax: +49-234-3214-188
E-mail: Gerhard.Link@ruhr-uni-bochum.de

Hi Hiro,

Nice to hear from you again. I'm glad everything is going well for you -
except for this sigma factor nomenclature issue which is giving everyone a
big headache.

First of all, I am willing to go along with whatever nomenclature is
decided upon for Arabidopsis. I like your idea of numbering the sigma
factors rather than using letters. I also like the idea that the numbers
should reflect the order in which the sigma factors were discovered, and
where two or more labs made simultaneous discoveries, the lab that
published first should have the honor of deciding the numbering order. I
agree with Bob Troxler that, when it comes to naming plant sigmas, we
shouldn't worry too much about using E. coli as a ruler, i.e. if we find a
"principal" plant sigma factor, we don't absolutely HAVE to call it Sig1.
It is obvious to everyone that the process of gene discovery is much faster
than the functional characterization of discovered genes, and we can't wait
for the functional studies to name the discovered genes. That would not be
practical!

So much for Arabidopsis. Regarding nomenclature for sigmas of other plants
species, I have a problem with Carl's proposed nomenclature. It may be
academically correct but it is just TOO cumbersome. What lab is going to
follow this extremely long and tedious naming system? For example, who is
voluntarily going to name the tobacco sigmas "NICta;Sig1;1", and
"NICta;Sig1;2" rather than NtSig1A and NtSig1B. Many labs have already
named their factors with an appropriate two-letter species name
designation, and so should be in agreement with a simple nomenclature of a
two-letter species code (e.g. At for Arabidopsis, Nt for Nicotiana tabacum,
Os for Oriza sativum, Zm for Zea mays, etc.) followed by a number
designating the order in which the sigma factor was discovered.

Regarding the numbers assigned to sigma factors of different plant species,
I don't think we should try too hard to match the sigmas of other species
closely to the sigmas of Arabidopsis. According to your phylogenetic tree
(with which I agree completely), Troxler's sigma factors should be named
ZmSig2A and ZmSig2B, whereas our three should be named ZmSig6 (original
name ZmSig3), ZmSig1A (original name ZmSig1) and ZmSig1B (original name
ZmSig2). This nomenclature falsely infers that our ZmSig1 and ZmSig2 are as
closely related as Troxler's ZmSig1 and ZmSig2. While our ZmSig1 and ZmSig2
may be related at the phylogenetic level, they are quite distinct at the
sequence level. This is different from Troxler's two factors which are
extremely closely related at the sequence level, bearing long stretches of
nearly 100% amino acid identity. You can see that this naming system does
not seem ideal, and I would like to get Troxler's input on this issue. I
would be happiest with just numbering the sigmas from other species in the
order in which they were published. If the publication dates are similar,
as was the case for the five maize sigma factors, I am sure the labs
involved can come to some sort of "gentleman's agreement" on who has to do
the renaming.

WHATEVER HAPPENS WITH THIS ISSUE WE NEED TO GET EVERY LAB TO FOLLOW THE
PROPOSED NOMENCLATURE. I feel this is very important. If even one lab calls
the Arabidopsis sigmas by a different name, then there seems no point in
having a unified nomenclature.

Best of luck on this issue,

Lori

Lori A. Allison
Assistant Professor
Department of Biochemistry
N258 Beadle Center
University of Nebraska
Lincoln, NE 68588-0664
phone: 402-472-0297
fax: 402-472-7842

Dear Lori Allison, Silva Lerbs-Mache, Gerhard Link, Kan Tanaka, and
Robert Troxler:

I thank all of you for your cooperation to have sent me your opinions
and comments on the nomenclature to find the consensus. I am below
attaching your e-mail messages for which I have obtained acceptance for
sharing the messages in the members in some cases but I have not yet
asked in the others.

In consideration of all thought, I have prepared the following draft of
the proposal of nomenclature of plant sigma factors associated with the
PDF file of the phylogenetic tree. I have already sent you an early or
near final version of the draft and the PDF file to hear your comments.
It is not easy to reach the consensus. I am describing an idea how we
should change the nomenclatures.

For Kobayashi (myself) and Lerbs-Mache of Arabidopsis:
In Tanaka's first publication, Allison's registration in the Genbank,
Link's nomenclatures in mustard, Tanaka's ones in tobacco and rice, and
nomenclatures in wheat and sorghum, "Sig1" or "SigA" is employed for
Kobayashi's and Lerbs-Mache's "SIG2". Therefore, the inverted
designation of SIG1/SIG2 must be considered. On the argument of the
"primary" or "principal" of sigma factors, the properties of SIG1
designated by Kobayashi and Lerbs-Mache most resemble those of E. coli
RpoD among SIG1, SIG2, and SIG3. However, SIG5 and SIG6 are more
closed to RpoD according to a phylogenetic tree (another version of the
tree, the version attached is on the comparison of whole peptide
regions) on the basis of comparison of regions 2.1 to 4.2 of sigma
factors. Therefore, classification with their features is reasonable
but is practically difficult at beginning stages of research.

For Tanaka:
Instead of nomenclatures such as "SigA", "SigB", and "SigC" etc., the
identification with digits is thought to be more adequate for the
following reasons: (1) the Commission on Plant Gene Nomenclature
(CPGN) as well as individual communities of gene nomenclature of plant
species such as Chlamydomonas, maize, and Arabidopsis, recommend
numbering the genes (see "Trends in Genetics, Genetic Nomenclature
Guide, 1995"); and (2) "SigA" of Arabidopsis and tobacco is not the
counterpart of "sigA" in bacteria among all sigma genes, resulting in
"Sig1" in plants is better for avoiding confusion.

For Allison and Troxler of maize:
Troxler thought that the easiest way to do it was to number sigma
factors (1, 2, 3, 4, 5 and 6) on the basis of publication date.
Allison would like to get Troxler's input on this issue and she
described that she would be happiest with just numbering the sigmas
from other species in the order in which they were published. One of
the idea is as Allison wrote: Troxler's sigma factors should be named
"ZmSig2A" and "ZmSig2B", whereas her three should be named ZmSig6
(original name ZmSig3), ZmSig1A (original name ZmSig1) and ZmSig1B
(original name ZmSig2). Is this kind of new nomenclatures finally
acceptable by Allison and Troxler?

For Link:
His nomenclatures of sigmas in mustard fit the proposed nomenclatures
here.

Concerning the submembers, one idea is to designate gene submembers
"NtSig1A" and "NtSig1B" (see Lori's comments below); another is a
proposal by CPGN, "NICta;Sig1;1" and "NICta;Sig1;2" (see Carl's
comments below). How do we handel the identification of submembers?

I am below attaching a draft of the report of proposal to CPGN named
with all of us. I would appreciate receiving your comments of change
and reconsideration or hopefully acceptance and agreement. On
receiving your reply, I could revise the proposal and send the final
version to CPGN.

Thank you very much again for your cooperation.

With best regards,

Hiro

Hirokazu Kobayashi
Laboratory of Plant Cell Technology
Graduate School of Nutritional and Environmental Sciences
UNIVERSITY OF SHIZUOKA
52-1 Yada, Shizuoka 422-8526, JAPAN
e-mail: hirokazu@smail.u-shizuoka-ken.ac.jp
http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/
phone: +81(Japan)-54-264-5582
fax: +81(Japan)-54-264-5584

=====================================================

PROPOSAL OF NOMENCLATURE OF PLANT SIGMA FACTORS
draft, October 14, 2000

Nucleotide sequences for sigma factors, key components in plastid-
encoded plastid RNA polymerase (PEP), were cloned and determined almost
simultaneously from each species at multiple laboratories in these
years. The sequence data were then registered in the GenBank and
published in journals with different nomenclatures for the same genes
especially in cases of Arabidopsis and maize. This made the confusion
in identification of genes and their products.

We, primary researchers of sigma factors, have analyzed the amino acid
sequence data registered in the GenBank to draw the detailed
phylogenetic tree of plant sigma factors with the proposal of
nomenclatures (attached hereto as a PDF file). We are also below
listing literatures published with original proposals of nomenclatures
of plant sigma factors. We have exchanged each thought by e-mail about
this issue and hopefully to find the consensus of nomenclatures (the
messages to be crucial for the final proposal below attached).

It has taken time to convince ourselves of the consensus of gene
nomenclature that makes some of us change our original nomenclature
published. We have reached the proposal of the following rules.

(1) Employment of common nomenclatures for counterparts throughout
different plant species.

(2) Numbering of sigma factors (1, 2, 3, 4, 5 and 6) on the basis of
priority of characterization or acceptance by the majority of
researchers.

On the second rule, the individual genes in different loci are also
identified with alphabets like "SigA", "SigB", and "SigC" proposed by
Kan Tanaka. The identification with digits is thought to be more
adequate for the following reasons: (1) the Commission on Plant Gene
Nomenclature (CPGN) as well as individual communities of gene
nomenclature of plant species such as Chlamydomonas, maize, and
Arabidopsis, recommend numbering the genes (see "Trends in Genetics,
Genetic Nomenclature Guide, 1995"); and (2) "SigA" of Arabidopsis and
tobacco is not the counterpart of "sigA" in bacteria among all sigma
genes, resulting in "Sig1" in plants is better for avoiding confusion.

Nomenclatures of members of sigma factors in tobacco and maize remain
to be concluded. One idea is to designate gene submembers "NtSig1A"
and "NtSig1B" (see Lori's comments below); another is a proposal by
CPGN, "NICta;Sig1;1" and "NICta;Sig1;2" (see Carl's comments below).

Working Group for Nomenclature of Plant Sigma Factors

Hirokazu Kobayashi, organizer
hirokazu@smail.u-shizuoka-ken.ac.jp

Lori Allison
lallison@unlnotes.unl.edu

Silva Lerbs-Mache
silva.lerbs-mache@ujf-grenoble.fr

Gerhard Link
gerhard.link@ruhr-uni-bochum.de

Kan Tanaka
kntanaka@imcbns.iam.u-tokyo.ac.jp

Robert Troxler
btrox@bu.edu

*********************************************
LITERATURES PUBLISHED WITH PROPOSALS OF NOMENCLATURE OF PLANT SIGMA
FACTORS
listed alphabetically of first authors' family names

L. A. Allison
The role of sigma factors in plastid transcription
Biochimie 82, 537-548 (2000)

M. Fujiwara, A. Nagashima, K. Kanamaru, K. Tanaka, and H. Takahashi
Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid
RNA polymerase sigma factors in Arabidopsis thaliana
FEBS Lett. 24078, 1-6 (2000)

M.-A. Hakimi, I. Privat, J.-G. Valay, and S. Lerbs-Mache
Evolutionary conservation of C-terminal domains of primary sigma70-type
transcription factors between plants and bacteria
J. .Biol. Chem. 275, 9215-9221 (2000)
[showing SIG4, SIG5, and SIG6]

K. Isono, M. Shimizu, K. Yoshimoto, Y. Niwa, K. Satoh, A. Yokota, and
H. Kobayashi
Leaf-specifically expressed genes for polypeptides destined for
chloroplasts with domains of sigma70-type factors of bacterial RNA
polymerases in Arabidopsis thaliana
Proc. Natl. Acad. Sci. U.S.A. 94, 14948-14953 (1997)

K. Kanamaru, M. Fujiwara, M. Seki, T. Katagiri, M. Nakamura, N.
Mochizuki, A. Nagatani, K. Shinozaki, K. Tanaka, and H. Takahashi
Plastidic RNA polymerase sigma factors in Arabidopsis
Plant Cell Physiol., 40, 832-842 (1999)

M. Kestermann, S. Neukirchen, K. Kloppstech, and G. Link
Sequence and expression characteristics of a nuclear-encoded
chloroplast sigma factor from mustard (Sinaous alba)
Nucleic Acids Res. 26, 2747-2753 (1998)

D. Kroll, M. Streubel, and P. Westhoff
A plastid sigma factor sequence from the C-4 monocot Sorghum bicolor
Plant Biology, 1, 180-186 (1999)

S. D. Lahiri, and L. A. Allison
Complementary expression of two plastid-localized alpha-like factors in
maize
Plant Physiol., 123, 883-894 (2000)

S. D. Lahiri, J. Yao, C. McCumbers, and L. A. Allison
Tissue-specific and light-dependent expression within a family of
nuclear encoded sigma-like factors from Zea mays
Mol. Cell Biol. Res. Commun. 1, 14-20 (1999)

K. Morikawa, S. Ito, Y. Tsunoyama, Y. Nakahira, T. Shiina, and Y.
Toyoshima
Circadian-regulated expression of a nuclear-encoded plastid sigma
factor gene (sigA) in wheat seedlings
FEBS Lett., 451, 275-278 (1999)

S. Tan, and R. F. Troxler
Characterization of two chloroplast RNA polymerase sigma
factors from Zea mays: Photoregulation and differential expression
Proc. Natl. Acad. Sci. USA, 96, 5316-5321 (1999)

K. Tanaka, Y. Tozawa, N. Mochizuki, K. Shinozaki, A. Nagatani, K.
Wakasa, and H. Takahashi
Characterization of three cDNA species encoding plastid RNA polymerase
sigma factors in Arabidopsis thaliana : evidence for the sigma factor
heterogeneity in higher plant plastids
FEBS Lett., 413, 309-313 , (1997)

Y. Tozawa, K. Tanaka, H. Takahashi, and K. Wakasa
Nuclear encoding of a plastid s factor in rice and its tissue- and
light dependent expression
Nucleic Acids Res., 26, 415-419 (1998)

J. Yao, L. A. Allison
The cDNA sequence of AtSIG4, a new member of the nuclear-encoded sigma
like factor gene family in Arabidopsis thaliana
Plant Physiol., 118, 1533 (1998)

Hi Hiro and everyone,

I have a clarification to make regarding the email that Hiro sent to us on
Saturday (Oct. 14). There was a misunderstanding of my intentions which can
be cleared up quickly.
Part of the email message stated:

For Allison and Troxler of maize:
Troxler thought that the easiest way to do it was to number sigma factors
(1, 2, 3, 4, 5 and 6) on the basis of publication date". Allison would
like to get Troxler's input on this issue and she described that she would
be happiest with just numbering the sigmas from other species in the order
in which they were published. One of the idea is as Allison wrote:
Troxler's sigma factors should be named "ZmSig2A" and "ZmSig2B", whereas
her three should be named ZmSig6 (original name ZmSig3), ZmSig1A (original
name ZmSig1) and ZmSig1B (original name ZmSig2). Is this kind of new
nomenclatures finally acceptable by Allison and Troxler?

In fact, I agree wholeheartedly with Bob that the maize SLFs should be
named in the order in which they were released in Genbank or published.
This issue of naming with A's and B' was something I brought up as an
argument AGAINST naming sigmas based on their phylogenetic relatedness.
That is to say, if the maize sigmas were named based on their current
positions on Hiro's phylogenetic tree, we would have to name Troxler's
sigma factors "ZmSig2A" and "ZmSig2B", whereas our three should be named
ZmSig6 (original name ZmSig3), ZmSig1A (original name ZmSig1) and ZmSig1B
(original name ZmSig2). This seems really confusing, therefore I would
argue strongly for naming factors in the order discovered RATHER than based
on phylogeny. Hope this clears up the issue (for maize at least).

Lori A. Allison
Assistant Professor
Department of Biochemistry
N258 Beadle Center
University of Nebraska
Lincoln, NE 68588-0664
phone: 402-472-0297
fax: 402-472-7842

Dear Lori, Bob, and colleagues:

I thank Lori for her correction and I am sorry for my last sentence that
made readers misunderstand her intention.

At 9:31 AM -0500 00.10.16, lallison@unlnotes.unl.edu wrote:
> Hi Hiro and everyone,
>
> I have a clarification to make regarding the email that Hiro sent to us on
> Saturday (Oct. 14). There was a misunderstanding of my intentions which
can
> be cleared up quickly.
[below deleted]

I thought in these months whether I should change our own nomenclature of
Arabidopsis sigma factors. If we employ common numbers for counterparts
throughout different plant species, I should invert our original SIG1 and
SIG2, because tobacco, mustard, rice, wheat, and sorghum designated the
counterparts of our original SIG2 as Sig1 or SigA. If we do not mind
commonly numbering sigma factors in different plant species, necessity for
inverting our numbers may be lowered. However, I think that it is desired
to try to designate counterparts with the same numbers.

As far as I know, Lori's and Bob's papers were coincidentally published
both in April in 1999. The date of publication of Bob's PNAS paper was
April 27, although I cannot recognize the publication date of Lori's paper
(I had access to her paper in its online web site). Although I am not a
person who decide the nomenclatures of maize sigmas, one of ideas might be:

Lori's
ZmSig1 -> ZmSig2A
ZmSig2 -> ZmSig2B
ZmSig3 -> ZmSig3

Bob's
ZmSig1 -> ZmSig1A
ZmSig2 -> ZmSig1B

This might be an idea to be criticized, but the proposed "ZmSig1A" and
"ZmSig1B" belong to the same branch as Sig1 or SigA from other species in
the phylogenetic tree. If Lori and Bob do not like the classification with
"A" and "B", this idea must be thrown out.

Sincerely yours,

Hiro

Hirokazu Kobayashi
Laboratory of Plant Cell Technology
Graduate School of Nutritional and Environmental Sciences
UNIVERSITY OF SHIZUOKA
52-1 Yada, Shizuoka 422-8526, JAPAN
e-mail: hirokazu@smail.u-shizuoka-ken.ac.jp
http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/
phone: +81(Japan)-54-264-5582
fax: +81(Japan)-54-264-5584

Dear "sigma searchers"

For my opinion, the sense of this discussion is to make it easy for
outsiders to read future papers dealing with the subject and to
understand what is going on with plant sigmas. To assure this, it
would help very much if AtSIG1 corresponds to ZmSIG1, ZmSIG1
corresponds to SaSIG1, SaSIG1 corresponds to TaSIG1 etc. I completely
agree with a sigma nomenclature based on a phylogenetic tree as
proposed by Hiro. I also agree to change our naming of SIG1 once
again to adapt it to the majority. What is important is the
understanding of the reader of our papers. The satisfaction to have
published at first (which is very understandable in regard of the
hard work of scientists nowadays and the difficulties to publish)
should be of second order.

At present, even the students in my lab that are familiar with the
problem have difficulties to find through the jungle. We should have
mercy with those that are not in the field. For my students, I
prepared a table where they can find that our SIG1 (SIG2 in the new
nomenclature) corresponds to Lori's SIG1 and SIG2; Our SIG2 (SIG1 in
the new nomenclature) corresponds to Bob's SIG1 and SIG2 and finally,
our SIG6 corresponds to Lori's SIG3. To avoid that readers have at
first to sort out the sequences from the databank and then to align
them in order to know their relations: Lori's SIG1 and SIG2 should be
named ZmSIG2A and ZmSIG2B (or ZmSIG2;1 and ZmSIG2;2 as you like);
Bob's SIG1 and SIG2 should be named ZmSIG1A and ZmSIG1B (or SIG1;1
and SIG1;2) and Lori's SIG3 should be named ZmSIG6.

With best regards,
Silva--

S. Mache,
Directrice de l'UMR 5575
Laboratoire de Genetique Moleculaire des Plantes
Universite Joseph Fourier
BP 53
38041 Grenoble Cedex 9
FranceTel: 04 76 63 57 44; fax: 04 76 51 43 36;
e-mail: Silva.Lerbs-Mache@ujf-grenoble.fr

Dear Sigma Colleagues,

The proposal to name sigma factors from different species based on their
phylogenetic relationships to the Arabidopsis sigma factors appears to have
strong support. Therefore, I will agree to this proposal and will re name
our ZmSig1 as ZmSig2A, ZmSig2 as ZmSig2B, and ZmSig3 as ZmSig6. This only
makes sense if Bob is in agreement with the name change. In this case, as I
understand from Hiro's tree, Bob's Sig1 would be renamed Sig1A (ZmSig1A?)
and Sig2 would be renamed Sig1B (ZmSig1B?). Are we all in agreement here?

And since I personally do not have the programs and expertise here to run
these trees routinely, I have asked Hiro to run any new sigma sequences
through the tree program as soon as they become available. That way we can
name the new sigmas without too much delay. I believe he agreed to do this-
right Hiro?

Lori

Lori A. Allison
Assistant Professor
Department of Biochemistry
N258 Beadle Center
University of Nebraska
Lincoln, NE 68588-0664
phone: 402-472-0297fax: 402-472-7842

Dear Silva, Lori, Bob, and Other Colleagues:

E-mail messages from Silva and Lori on Friday and Saturday (in Japanese
time) very much encouraged me in the point that my effort to find the
unified nomenclatures of plant sigma factors was not meaningless, and I
thank both of them for their considering this problem to be resolved and
sending their messages.

I am sorry for my slow response. Meanwhile, it has taken time to fix my
computer after assembling a new hard disk into it, when I was unable to
respond to them.

I also received e-mail messages from Kan Tanaka with a sort of agreement to
number sigma factors. His messages were written in Japanese, and I here
translate their outline into English.-

- - - - - - - - - - - - - - - - - - - - - - - - - - -

At 10:30 AM 00.10.18, Kan Tanaka wrote (a part of messages translated):

I do basically not have any critiques for the proposed nomenclature. Will
you publish this proposal in any journal with our authorship? When will
this proposal become valid?

By the way, E. coli rpoS is described as sigS in the PDF file that I
received. I have probably seen such a nomenclature, "sigS", but I am sureit
is not accepted in the community. I think "sigS" must be "rpoS"-

- - - - - - - - - - - - - - - - - - - - - - - - - - -

At 2:22 AM 00.10.19, Hirokazu KOBAYASHI wrote (a part of messages
translated):

The proposal would be mounted on the web page of CPGN:

http://mbclserver.rutgers.edu/CPGN/

I think this proposal would be valid after getting a consensus by a
majority of primary researchers.

I thank you very much for your comment of "sigS". Since I recognize the
following review article to be well written where "sigS" is adopted, I
described "sigS" in my PDF file. I will change "sigS" to "rpoS" when I
would submit the file to CPGN.

M. Lonetto, M. Cribskov, and C. A. Gross: The sigma70 family: Sequence
conservation and evolutionary relationships. J. Bacteriol., 174,
3843-3849, 1992-

- - - - - - - - - - - - - - - - - - - - - - - - - - -

I want to hear Bob's thought about nomenclatures of maize sigma factors
(refer to Lori's last messages). After receiving Bob's reply, I would
revise the proposal and again send it to these members to hear further
comment, if any.

I may do my best to assign new entries of sigma factors to the groups in
the phylogenetic tree, although it may not be practically easy how soon we
find out the new entries before their publication in journals. I will
consult with Carl Price, the chief of CPGN, about this problem.

With best regards,

Hiro

Hirokazu Kobayashi
Laboratory of Plant Cell Technology
Graduate School of Nutritional and Environmental Sciences
UNIVERSITY OF SHIZUOKA
52-1 Yada, Shizuoka 422-8526, JAPAN
e-mail: hirokazu@smail.u-shizuoka-ken.ac.jp
http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/
phone: +81(Japan)-54-264-5582
fax: +81(Japan)-54-264-5584

[deleted]

At 2:55 AM +0900 00.10.31, Hirokazu KOBAYASHI wrote:
> Thank you for your waiting for our proposal with the consensus of the
sigma
> nomenclature.
>
> Among primary researchers working of sigma factors, who named the same
> factors with different names: for sigmas from Arabidopsis, Kan, Silva,
> and myself; and for sigmas from maize, Lori and Bob, we (except for Bob
> who has not yet replied me) have agreed that we employ common
> nomenclatures for counterparts throughout different plant species
> following the proposal indicated in the phylogenetic trees drawn by me
> before. I am below attaching our e-mail messages serially.
>
> I have two questions.
>
> (1) How widely the proposal would be distributed. May I understand that
> the proposal would be mounted on the web page of CPGN, which would be
> announced to plant researchers in several mailing lists? This was also
> Kan's question (see his messages below).

First, the proposal will be mounted on the CPGN's Web site.
Then it will be presented to the CPGN associates, about 300 scientists world
wide, who are drawn principally from the various working groups. We normally
allow two weeks for associates to respond, and we post their responses on
the same Web page. If there are no substantive objections, the proposal is
then listed as "approved" by the CPGN.

In addition, Ellen is preparing an abbreviated version of the Mendel
database that can be downloaded by FTP. We shall announce this to journals
so their editorial boards--and of course any scientist--can have ready access
to the CPGN recommendations.

> (2) We should do our best to assign new entries of sigma factors to the
> groups in the phylogenetic tree to avoid the confusion of nomenclatures.
> Is there any way governed by CPGN to find out the new entries before their
> publication in journals. This was also raised by Lori (see her messages
below).

Our sources for new accessions are the sequence databases, and they defer to
authors' requests not release the entries until after publication.

> We are waiting for Bob's thought. If we de not receive his reply, I would
> send you the report to be mounted on the web page without his name in this
> authorized group. I am anxious that Lori might not follow the proposal
> when Bob does not.

[deleted]

I thank you very much for your answers to my questions. I now understand
the activity of CPGN more clearly. I think that each nomenclature of gene
must be authorized when a majority of people adopt that in their
publications. In this point, the consensus of proposal of sigma
nomenclature in which we employ the same numbers for counterparts
throughout the plant species must be the goal, although we have not yet
obtained Bob Troxler's agreement. I will contact him again. If I do not
have his approval, I would ask you to mount our proposal without his name
on the CPGN web page.

[deleted]

Dear Bob:

I would appreciate hearing your thought about the nomenclatures of sigma
factors from maize. Did you receive e-mail messages sent by me on October
24 (in Japanese time)?

I was asked by Carl in last May and Pal Maliga forced us to find unified
nomenclatures. I, therefore, surveyed nomenclatures registered in the
GenBank to analyze the homology. I made sure that we can classify the
sigma factors into 6 groups on the basis of sigma factors from Arabidopsis.
Kan, Silva, and myself have decided to change our original nomenclatures to
employ unified ones for Arabidopsis sigma factors. Lori said that she
might change her original nomenclatures for maize sigma factors following
numbers of sigma factors from Arabidopsis. Since I want to finish this
task for the nomenclature, I would appreciate hearing your thought.

I am here listing dates of publication and registration of your and Lori's
sequences.

- - - - - - - - - - - - - - -

S. Tan, and R. F. Troxler
Characterization of two chloroplast RNA polymerase sigma
factors from Zea mays: Photoregulation and differential expression
Proc. Natl. Acad. Sci. USA, 96, 5316-5321, 1999

Received: December 15, 1998
Communicated: March 15, 1999
Published: April 27, 1999

Dates of submission to the GenBank:
sig1: April 8, 1998
sig2: April 8, 1998

S. D. Lahiri, J. Yao, C. McCumbers, and L. A. Allison
Tissue-specific and light-dependent expression within a family of nuclear
encoded sigma-like factors from Zea mays
Mol. Cell Biol. Res. Commun. 1, 14-20 (1999)

Received: January 5, 1999
Published: April, 1999

Dates of submission to the GenBank:
sig1: October 19, 1998
sig2: October 19, 1998
sig3: October 19, 1998

- - - - - - - - - - - - - - -

I cannot identify the date of publication of Lori's paper on the online
journal page of Mol. Cell Biol. Res. Commun. only to which I can access.

[deleted]

Another point to be considered is that mentioned by Silva.

- - - - - - - - - - - - - - -

Date: Thu, 19 Oct 2000 19:37:11 -0700
To: lallison@unlnotes.unl.edu, btrox@bu.edu, silva.lerbs-mache@ujf
grenoble.fr,gerhard.link@ruhr-uni-bochum.de, kntanaka@imcbns.iam.u
tokyo.ac.jp,hirokazu@smail.u-shizuoka-ken.ac.jp
From: Silva LERBS-MACHE <Silva.Lerbs-Mache@ujf-grenoble.fr>
Subject: sigma nomenclature
Dear "sigma searchers"
For my opinion, the sense of this discussion is to make it easy for
outsiders to read future papers dealing with the subject and to
understand what is going on with plant sigmas. To assure this, it

[deleted]

- - - - - - - - - - - - - - -

Lori said on responding Silva's opinion.

- - - - - - - - - - - - - - -

From: lallison@unlnotes.unl.edu
Subject: Re: sigma nomenclature
To: Silva LERBS-MACHE <Silva.Lerbs-Mache@ujf-grenoble.fr>
Cc: btrox@bu.edu, gerhard.link@ruhr-uni
bochum.de,kntanaka@imcbns.iam.u-tokyo.ac.jp, hirokazu@smail.u shizuoka
ken.ac.jp
Date: Fri, 20 Oct 2000 10:55:29 -0500

Dear Sigma Colleagues,

The proposal to name sigma factors from different species based on their
phylogenetic relationships to the Arabidopsis sigma factors appears to have
strong support. Therefore, I will agree to this proposal and will re name
our ZmSig1 as ZmSig2A, ZmSig2 as ZmSig2B, and ZmSig3 as ZmSig6. This only
makes sense if Bob is in agreement with the name change. In this case, as I
understand from Hiro's tree, Bob's Sig1 would be renamed Sig1A (ZmSig1A?)
and Sig2 would be renamed Sig1B (ZmSig1B?). Are we all in agreement here?

- - - - - - - - - - - - - - -

How do you think about this opinion?

I would appreciate hearing your comments or thought to finish my task.

Thank you very much for your cooperation. I also wish good luck on your
research.

With best regards,

Hiro

Hirokazu Kobayashi
Laboratory of Plant Cell Technology
Graduate School of Nutritional and Environmental Sciences
UNIVERSITY OF SHIZUOKA
52-1 Yada, Shizuoka 422-8526, JAPAN
e-mail: hirokazu@smail.u-shizuoka-ken.ac.jp
http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/
phone: +81(Japan)-54-264-5582
fax: +81(Japan)-54-264-5584

Dear Hiro,

I don't know why I couldn't access the jpg files, but I took a third
look and was able to access sigma-medium.jpg (and sigma-small but not
sigma-large). In any event, your phylogenetic tree--and a revised text
for the Sigma home page--should be up on the Web site
(http://mbclserver.rutgers.edu/CPGN/SigmaFactorWeb/Sigma.group.html)
within an hour.

As far as I can see, all that is missing is your group's proposal; I
know you are waiting to hear from Bob Troxler, but please check the site
for errors and omissions. For example, should Bob Haselkorn be listed in
the Working Group?

Dear Hiro,

I was reviewing the proposal sent in your message of 10 October. I
realize that this was sent to your colleagues concerned with sigma
factors, and will doubtless be revised before presentation to the
scientific public.

This is presumptuous of me, and I apologize in advance, but I thought I
might help by offering some suggestions for the final document. So, I am
appending an html version, such as might be presented to the CPGN
associates.

Again, I hope that I am not intruding.

Best,--

Carl

[deleted]

At 11:54 AM -0800 00.11.2, Carl Price wrote:
>sigma-large). In any event, your phylogenetic tree--and a revised text
>for the Sigma home page--should be up on the Web site
>(http://mbclserver.rutgers.edu/CPGN/SigmaFactorWeb/Sigma.group.html)
>within an hour.
>
>As far as I can see, all that is missing is your group's proposal; I
>know you are waiting to hear from Bob Troxler, but please check the site
>for errors and omissions. For example, should Bob Haselkorn be listed in
>the Working Group?

I have accessed to the web page and I knew what you made. I think that
there are several problems. The most crucial one is that I have not yet
got approval of all members that you listed about the contents of this
page. I told Lori, Silva, Gerhard, and Kan that we would mount the page in
the official CPGN web site with their final agreement. I made sure that
the page of sigma factors has already opened to the public: this page has
been linked from the front page of the CPGN. Therefore, I ask you to once
disconnect the sigma page from the front page to wait for their approval.
Alternatively, I propose you to replace the present page with a revised
version, which shows minimal approved contents and I will make it in this
week end.

Another problem that we must resolve is the part of sigma factors from
cyanobacteria and primitive eukaryotic alga which are in other branches
that those of higher plants. I think that we should split sigma factors
into two groups of those from higher plant and ones from cyanobacteria and
primitive eukaryotic alga. Therefore, I think that we should divide your
tables of "Association of gene families with product families" and "List of
accessions encoding sigma factors" into two parts of higher plants and the
others. I am not working on sigmas from primitive organisms, and I have
consulted with Kan Tanaka about his contribution to unify the nomenclatures
of such sigmas but I have not yet received his positive reply. Bob
Haselkorn, Susan Golden, or Arthur Grossman must be a person who takes this
task. I may contact them, if you think that I should do.

A question that I want to make sure is definition of "gene family". On
your web page, you define "Sig1" to "Sig6" as each individual gene family
(is this understanding correct?). On the other hand, there may be another
concept that "Sig1" to "Sig6"are members of the "Sig" gene family. Why
did you adopt the former definition? Is the later definition is wrong? If
so, why?

with best regards,

Hiro

Dear Hiro,

A brief reply:

I have removed the link between the CPGN home page and the Sigma page.This
means that you can access the Sigma page, since you have the URL, but it
will not be visible to others browsing the CPGN Web site.

Second, the CPGN defines "gene family" as "all genes across the plant
kingdom that encode similar products and have similar coding sequences
comprise a single gene family." Now, this need not be everyone's definition
of a gene family, but we find it convenient. We could use a term to
describe collections of genes that encode similar products but including
genes with non-similar coding sequences. Maybe "superfamily." In addition
to the Sig superfamily, there would be many examples, including the Lhc
genes encoding light-harvesting proteins (Lhca1-6 and Lhcb1-6).

[deleted]

[deleted]

At 8:16 AM -0800 00.11.3, Carl Price wrote:
[deleted]

>Second, the CPGN defines "gene family" as "all genes across the plant
>kingdom that encode similar products and have similar coding sequences
>comprise a single gene family." Now, this need not be everyone's
>definition of a genefamily, but we find it convenient. We could use a
>term to describecollections of genes that encode similar products but
>including genes with non similar coding sequences. Maybe "superfamily."
>In addition tothe Sig superfamily, there would be many examples,
>including the Lhcgenes encoding light-harvesting proteins (Lhca1-6
>and Lhcb1-6).

Thank you for the explanation. I understand the point, but a further
question is the definition of "similarity". In the case of higher plant
sigmas, these have the common sequences in the conserved region so called
"Regions 2.1 to 4.2", but genes for 6 sigmas from Arabidopsis are not
hybridized each other. In this kind of situation of 6 sigmas, they have no
similarity in your definition. Am I right?

Sincerely,

Hiro

[deleted]

On the topic of "sequence similarity," you ask a very pertinent
question. What are the criteria of sequence similarity? The simple
answer is that, in our usage, it is arbitrary. But the true answer is
more complicated and somewhat political: When David Lonsdale was
manager of the Mendel database, he introduced the idea of sorting all
of the sequences then in SwissProt into mutually exclusive sets based
on sequence similarity. His idea was that these sets would define "gene
family."

David's idea was very productive, but we quickly discovered that his
"gene families" did not always correspond to gene families as
recognized by people in the field. David withdrew from the CPGN in
January 1999, and, after resuming management of Mendel, we renamed
these sets "product families" and returned "gene families" to the
preferences of the people in the working groups.

But David continued to publish his version of things under the name
"Mendel GFDb." We sought some level of cooperation in which we would
agree on what accessions fell into our "product families" equal to his
"gene families." David has refused any communication, but we decided
that confusion would be minimized if we maintained that equivalency
except in instances where GFDb was empty of the genes in question or
where there were obvious errors.

The bottom line is that we are perfectly happy if working groups decide
to subdivide a product family, but we prefer not to have gene families
include two or more product families.

Back to the six sigmas: Sig1, Sig2, and Sig3 happen to fall into three
product families: 3325, 3191, and 3169 that have been identified by
David Lonsdale's group. David's database is empty of Sig4, Sig5, Sig6,
so we do not have a product family for them.

It's a long answer, but I hope it is intelligible.--

Carl

[deleted]

Later today I expect to send an announcement to the CPGN associates,
that's all of you, of the mounting of release 8.0 of Mendel. I shall
also ask people to examine it for errors.

Along with the hundreds of other gene family names, the sigma factors
are listed there, but without any indication of a specific proposal.
Among a number of errors I discovered that sigma factors are listed
under RNA polymerase with Tom Guilfoyl as working group organizer.
Sorry about that.--

Carl--

C. A. Price
7521 Brava Street
La Costa, CA 92009-7504, USA
price@onemain.com
price@mbcl.rutgers.edu (can receive only)
ph: 1-760-942-6050
fax: 1-760-479-0259 (please telephone 1-760-942-6050 first)

Dear Hiro:

thank you for letting me know about the final outcome of the sigma
discussion. To me your report looks pretty final, it presents a
balanced view of the data, and it will help clarifying the issues
involved now and in the future. Thank you for your time and effort.

Kind regards,

Gerhard

Gerhard Link,
University of Bochum,
Plant Cell Physiology,
D-44780 Bochum,
Germany
Phone: +49-234-322-5495
Fax: +49-234-3214-188
E-mail: Gerhard.Link@ruhr-uni-bochum.de

Dear Hiro:

I congratulate you on you excellent efforts to obtain a consensus for
nomenclature on sigma factors in plants. I apologize for not replying
sooner.

For me, it seems reasonable to name sigma factor proteins: SIG1, SIG2,
SIG3, etc., preceded by the abbreviation of genus and species: At, Zm,
etc.

I think it is not a good idea to name sigma factors based on sequence
similarity in your elegant evolutionary tree. Not all investigators may
have access to the software to analyze their sequence data in that way
and it seems unreasonable for the discoverer of a sigma factor to be
obliged to ask a colleague for the correct name of his/her sigma
factor.

Therefore, I think sigma factors should be numbered in order of their
discovery. This has worked well in other fields. An example I am
familar with is the human mucins: MUC1, MUC2, MUC3, up to MUC12, named
in their order of discovery (publication date) and differentially
expressed in salivary glands and the respiratory tree,
gastrointenstinal tract and genitourinary tracts.

If sigma factors were to be numbered in order of their discovery, I
think priority should be based on either GenBank accession date or date
of receipt of a published manuscript. In my view, this would be the
fairest approach to the nomenclature.

Possible problems with this approach might be (a) rigor of the review
process for invited publications and (b) short turnaround times for
some rapid publication journals. One could argue that this might favor
priority based on GenBank accession date.

On biological grounds, it seems to me that it is diffucult to make
functional comparisons between plant sigma factors and those in
bacteria. I think it is unlikely that plants have a functional
homologue of sigma 70 in E. coli (transcription of housekeeping genes
during log phase growth). The situation in plants seems much more
complex considering (a) dicots vs. monocots, (b) leaves vs. stems vs.
flowers vs roots, and (c) parameters influencing differential
expression of sigma factors such as stress, development, senescence,
etc.

Finally, I no longer work on plant sigma factors and do not wish to be
an obstructionist regarding the nomenclature. Therefore, I would be
inclined to endorse the consensus of the majority.

With kindest regards.

Bob

Dear Bob:

[deleted]

I well understand that the nomenclature of sigma factors based on their
similarity has problems. However, this way of nomenclature would has an
advantage of recognizing each factor in different plant species, if this
works ideally. For the following two reasons, I think that we would adapt
the nomenclatures with common numbers to identify sigma factors: (1) a
majority of persons with whom I have consulted would have indicted their
approval of nomenclature in this way; and (2) this also satisfies the
classification proposed by the CPGN (see Carl's messages).

I think that we should record your thought that it is the most reasonable
to number sigma factors in order of their discovery on the web page of
proposal.

I have just mounted a temporal version of proposal on the below web page.
Similar contents would be shown on the formal web page of the CPGN on our
agreement. I would appreciate hearing your further comments and approval.

http://dfns.u-shizuoka-ken.ac.jp/labs/pctech/sigma/proposal/

[deleted]

Hiro