― 50 ―

Head

Experimental Plant Division

Goal

Activities

Plant science is vital for food production and environmental

protection. The aim of this laboratory is to promote plant

science through the collection and distribution of plant

resources. In order to achieve this aim, we participate with

the National Bioresource Project (NBRP) and distribute

Collection, preservation and distribution of Arabidopsis

seeds, plant cultured cells and plant DNA materials

Development of novel techniques for the establishment,

preservation, characterization and utilization of plant

resources

MembersHead

Masatomo KOBAYASHI, Ph.D. (2001.4~)

Senior Visiting Scientist

Nobuharu GOTO, Ph.D. (2004.8~)

Senior Research Scientist

Hiroshi ABE, Ph.D. (2002.2~) Satoshi IUCHI, Ph.D. (2002.3~)

Toshihiro KOBAYASHI, Ph.D. (2002.10~)

Visiting Researcher

Yuriko KOBAYASHI, Ph.D. (2008.4~)

Technical Staff Ⅱ

Kanako ISHIYAMA (2001.4~) Issei SASAKI (2001.4~)

Tomoko UCHIDA (2001.4~) Yuri SHITOMI (2008.4~)

Assistant

Shiori OTA (2001.6~) Norie TSUDA (2007.4~2007.11)

Agency Staff

Setsuko KAWAMURA (2001.4~) Mayumi SUGAWARA (2001.10~)

Fumie MORI (2003.3~) Atsuko IUCHI (2003.4~)

Toshiko NAKAYAMA (2005.6~2006.12) Yukie ASO (2005.11~)

Mariko ISSHIKI (2007.7~2008.2) Aki YAMAMOTO (2008.2~)

Atsuko MURASUGI (2007.4~)

Arabidopsis seeds, plant DNA materials and plant cultured

cells to the international community of plant science. We also

develop novel techniques for the establishment, preservation,

characterization and utilization of bioresources as well as

conduct technical training courses.

1.

2.

Promotion of training courses on the handling and

advanced use of plant resources

3.

Masatomo KOBAYASHI, Ph.D.

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 51 ―

Abe, Inaba, Kizara, Yoshida, Nemoto, Uchida, Aso, Kawamura, Iuchi(A), SasakiKitabayashi, Takahashi, Kobayashi(Y), Murasugi, Mori, Ishiyama, Yamamoto, Akaishi

Iuchi(S), Sugawara, Kobayashi(M), Ota, Kobayashi(T)

Specific Aims

I. Collection, preservation and distribution of plant resources

The core resources that we preserve are materials of

Arabidopsis thaliana, the most popular model plant in

the world. We extensively collect and distribute genomic

materials such as seeds of insertion mutants and full-length

cDNA clones of Arabidopsis. We also collect and preserve

cDNA clones of other model plants, such as Physcomitrella

patens. As a result of genome projects on model plants like P.

patens, cDNA clones are increasingly becoming a key tool in

developing novel knowledge of the plant kingdom and thus

are regarded as valuable resources for various fields of plant

research.

Global contribution is an important feature of our project. To

date, more than 1,500 laboratories and research groups in over

40 countries and areas have registered as our users. Currently,

we have approx. 540,000 accessions of preserved Arabidopsis

seeds, plant cultured cell lines and DNA materials. Since

2002, we have distributed more than 27,000 plant materials

to the international research community. We devote our

efforts to control the quality of the resource by operating

quality examination of all materials before shipment. We have

received not only many thanks from our users to whom we

have sent materials but also a special prize from The Botanical

Society of Japan (in 2005). Now, this division not only leads

the plant resource project in Japan but also has become one of

the distinguished plant resource centers in the world.

1) Arabidopsis seeds

Arabidopsis transposon-tagged mutants established by RIKEN

Genomic Sciences Center (GSC) as well as Arabidopsis

activation-tagged mutants established by RIKEN Tsukuba

Institute and RIKEN GSC are preserved and distributed. The

transposon-tagged line is suitable for reverse genetics because

the insertion site of the transposable (Ds) element has been

characterized, while the activation-tagged line is suitable for

phenotype screening (forward genetics). In order to improve

the value of the transposon-tagged mutants, we are preparing

seed pools that are homozygous for the Ds insertion. We

are also preparing seeds of Arabidopsis Full-length cDNA

OvereXpressing (FOX) lines recently established by RIKEN

Plant Science Center (PSC).

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 52 ―

In addition to the mutant lines mentioned above, the

Arabidopsis Information Service (AIS) collection of

Arabidopsis seeds formerly preserved in The Sendai

Arabidopsis Seed Stock Center (SASSC) has been deposited

in our center. The AIS collection is well-known because

AIS was the first organization that distributed seeds of wild-

type Arabidopsis. Currently, nearly 400 natural accessions of

Arabidopsis that are useful for research on QTL are available

from our center. The revision of the SASSC database is under

the way, and users will be able to know detailed features of

natural accessions through our web page.

2) Plant DNA materials

Full-length cDNA is important for post-genome research,

since it is useful in the production of transgenic plants

and functional proteins. We preserve and distribute full-

length cDNA clones of four plant species, namely, RIKEN

Arabidopsis full-length cDNA (RAFL) clones (from RIKEN

GSC), Physcomitrella patens (model moss) full-length cDNA

clones (from the National Institute of Basic Biology), poplar

(model tree) full-length cDNA clones (from the Forestry

and Forest Products Research Institute), and cassava full-

length cDNA clones (from RIKEN PSC). The RAFL clone is

regarded as a world standard resource and used in hundreds

of laboratories. We have established the SABRE (Systematic

consolidation of Arabidopsis and other Botanical REsource)

database to utilize these valuable resources. Through the

SABRE database, users can access the genomic information of

Arabidopsis in TAIR (The Arabidopsis Information Resource)

that will provide references on the function of the genes of

interest.

3) Plant cultured cells

We preserve and distribute cultured cell lines of model plants

such as Arabidopsis, rice, tobacco, and Lotus japonicum.

Among them, tobacco BY-2 and Arabidopsis T87 cells are

the most popular cell lines. At present, we distribute none

of these materials abroad because of the expected damage

in living cells during transport. We are currently examining

the procedure for overseas shipment so that international

community can utilize these valuable resources in the near

future.

II. Technological Development

1) Technological development for the preservation of plant

cultured cells and DNA materials

Cultured cells are maintained as living cells and are difficult

to preserve in liquid nitrogen. Recently, we have established

a cryopreservation protocol for tobacco BY-2 and T87 cells.

(Ref. 1) We are now going to apply the protocol to the

preservation of the recently deposited transgenic cell lines.

Novel technologies for the long-term preservation of DNA

materials are under development with support from NBRP to

reduce the labor and cost for the maintenance of this resource.

2) Development of genomic resource and technologies that

promote crop research

Agriculture is a major industrial field in which results of plant

research are utilized. To improve agricultural production, crop

research should be intensively promoted. In collaboration with

RIBS (Research Institute for Biological Sciences, Okayama),

we have developed cDNA clones of Chinese cabbage (Brassica

rapa). We use these materials to establish a test array

system for evaluating effects of chemical compounds on the

activation of plant immune systems. We also use Arabidopsis

to identify novel genes that act in stress response.

　Furthermore, RIKEN BRC and Gifu University reported

an Arabidopsis gene, STOP1, that plays a key role in acid-

and aluminum-stress signals (Ref. 14). Our studies not only

improve the value of Arabidopsis resources and information

but also promote agricultural research to increase the crop

production.

3) Characterization of natural accessions and homozygous

transposon-tagged lines

Natural accessions are useful for research on biotic and

abiotic stresses. However, phylogenetic information on these

materials have been mostly unavailable. Approximately 400

natural accessions of Arabidopsis are preserved in RIKEN

BRC, and we have analyzed their phylogenetic background

using a marker system with a simple sequence length

polymorphism. We also characterize their response of natural

accessions and homozygous transposon-tagged lines against

various stresses to improve the value of these resources. These

data will be opened to public through our web page.

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 53 ―

BY-2 and T87 as model plant cell linesTobacco BY-2 cell line is a well known plant cultured cell that was established in Japan. Arabidopsis T87 cell line is used for the research on photosynthesis and circadian rhythm because it develops chloroplast under light condition.

Natural accessions preserved in RIKEN BRCWe preserve over 400 natural accessions of Arabidopsis and related species. Characterization of these plants are in progress.

III. Training course

Since 2004, we have operated training courses on basic and

advanced techniques required for the transformation and

preservation of plant cultured cells. In 2007, a training course

on basic techniques for the cultivation and transformation

of Arabidopsis was also carried out. A total of forty-fivr

researchers and students from universities, research institutes

and private sectors have joined the program.

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 54 ―

Kobayashi T., Niino T., Kobayashi M.: “Simple

cryopreservation protocol with an encapsulation

technique for tobacco BY-2 supension cell cultures.”

Plant Biotech. 22(2), 105-112 (2005).* (This manuscript

received the Best Article Prize from the Japanese Society

for Plant Cell and Molecular Biology in 2006.)

Itoh H., Sasaki A., Ueguchi-Tanaka M., Ishiyama K.,

Kobayashi M., Hasegawa Y., Minami E., Ashikari M.,

Matsuoka M.: “Dissection of the phosphorylation of rice

DELLA protein, SLENDER RICE1.” Plant Cell Physiol.

46(8), 1392-1399 (2005).*

Suzuki H., Ishiyama K., Kobayashi M., Ogawa T.:

“Specific expression of the gibberellin 3b-hydroxylase

gene, HvGA3ox2, in the epithelium is important for Amy1

expression in germinating barley seeds.” Plant Biotech.

22(3), 195-200 (2005).*

Ueguchi-Tanaka M., Ashikari M., Nakajima M., Itoh

H., Katoh E., Kobayashi M., Chow T.-Y., Hsing Y.-I.C.,

Kitano H., Yamaguchi I., Matsuoka M.: “GIBBERELLIN

INSENSITIVE DWARF1 encodes a soluble receptor for

gibberellin.” Nature. 437(29), 693-698 (2005).*

Katagiri T., Ishiyama K., Kato T., Tabata S., Kobayashi

M., Shinozaki K.: “An important role of phosphatidic

acid in ABA signaling during germination in Arabidopsis

thaliana.” The Plant J. 43, 107-117 (2005).*

Osakabe K., Abe K., Yamanouchi H., Takyuu T.,

Yoshioka T., Ito Y., Kato T., Tabata S., Kurei S., Yoshioka

Y., Machida Y., Seki M., Kobayashi M., Shinozaki K.,

Ichikawa H., Toki S.: “Arabidopsis Rad51B is important

for double-strand DNA breaks repair in somatic cells.”

Plant Mol. Biol. 57, 819-833 (2005).*

Ito Y., Katsura K., Maruyama K., Taji T., Kobayashi

M., Seki M., Shinozaki K., Yamaguchi-Shinozaki

K.: “Functional analysis of rice DREB1/CBF-type

transcription factors involved in cold-responsive gene

expression in transgenic rice.” Plant Cell Physiol. 47,

Publication

1.

2.

3.

4.

5.

6.

7.

【Original Papers】 (*Peer reviewed journals)

141-153 (2006).*

Umezawa T., Okamoto M., Kushiro T., Nambara E.,

Oono Y., Seki M., Kobayashi M., Koshiba T., Kamiya Y.,

Shinozaki K.: “CYP707A3, a major ABA 8'-hydroxylase

involved in dehydration and rehydration response in

Arabidopsis thaliana.” Plant J. 46, 171-182 (2006).*

Kobayashi T., Niino T., Kobayashi M.: “Cryopreservation

of tobacco BY-2 suspension cell cultures by vitrification

with encapsulation.” Plant Biotech. 23, 333-337 (2006).*

Nakajima M., Shimada A., Takashi Y., Kim Y., Park S.,

Ueguchi M., Suzuki H., Katoh E., Iuchi S., Kobayashi

M., Maeda T., Matsuoka M., Yamaguchi I.: “Identification

and characterization of Arabidopsis gibberellin

receptors.” Plant J. 46, 880-889 (2006).*

Narusaka M., Abe H., Kobayashi M., Kubo Y., Kawai

K., Izawa N., Narusaka Y.: “A model system to screen

for candidate plant activators using an immune-induction

system in Arabidopsis.” Plant Biotech. 23, 321-327

(2006).*

Narusaka M., Abe H., Kobayashi M., Kubo Y.,

Narusaka Y.: “Comparative analysis of expression

profiles of counterpart gene sets between Brassica

rapa and Arabidopsis thaliana during fungal pathogen

Colletotrichum higginsianum infection.” Plant Biotech.

23, 503-508 (2006).*

Kitahata N., Hang S., Noji N., Saito T., Kobayashi

M., Nakano T., Kuchitsu K., Shinozaki K., Yoshida

S., Matsumoto S., Tsujimoto M., Asami T.: “A 9-cis-

epoxycarotenoid dioxygenase inhibitor for use in

the elucidation of abscisic acid action mechanisms.”

Bioorganic & Medicinal Chemistry 14, 5555-5561

(2006).*

Iuchi S., Koyama H., Iuchi A., Kobayashi Y., Kitabayashi

S., Kobayashi Y., Ikka T., Hirayama T., Shinozaki K.,

Kobayashi M.: “Zinc finger protein STOP1 is critical

8.

9.

10.

11.

12.

13.

14.

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 55 ―

for proton tolerance in Arabidopsis and coregulates a

key gene in aluminum tolerance.” Proceedings of the

National Academy of Sciences of the United States of

America 104, 23 9990-9905 (2007).*

Iuchi S., Suzuki H., Kim Y., Iuchi A., Kuromori T.,

Ueguchi M., Asami T., Yamaguchi I., Matsuoka M.,

Kobayashi M., Nakajima M.: “Multiple loss-of-function

of Arabidopsis gibberellin receptor AtGID1s completely

shuts down a gibberellin signal.” The Plant Journal 50,

958-966 (2007).*

Kobayashi T., Kobayashi M.: “Cryopreservation of

cultured plant cells.” Japanese Journal of Plant Science 1,

7-11 (2007).*

Ikka T., Kobayashi Y., Iuchi S., Sakurai N., Shibata

D., Kobayashi M., Koyama H.: “Natural variation of

Arabidopsis thaliana reveals that aluminum resistance

and proton resistance are controlled by different genetic

15.

16.

17.

factors.” Theoretical and Applied Genetics 115, 709-7

(2007).*

Motohashi R., Yamazaki T., Myouga F., Ito T., Ito

K., Satou M., Kobayashi M., Nagata N., Yoshida S.,

Nagashima A., Tanaka K., Takahashi S., Shinozaki K.:

“Chloroplast ribosome release factor 1 (AtcpRF1) is

essential for chloroplast development.” Plant Molecular

Biology 64, 481-4 (2007).*

Abe H., Onishi J., Narusaka M., Seo S., Narusaka Y.,

Tsuda S., Kobayashi M.: “Function of jasmonate in

response and tolerance of Arabidopsis to thrip feeding.”

Plant Cell Physiology 49, 68-80 (2008).*

Narusaka Y., Narusaka M., Shiraishi T., Kawai K.,

Izawa N., Hatakeyama K., Abe H., Kobayashi M.: “The

effects of plant activators on leaf spot and anthracnose

of Chinese cabbage.” Journal of Pesticide Science 33,

196-200 (2008).*

18.

19.

20.

Oral Presentation

Niino T., Tanaka D., Kobayashi T.: “Utilization of plant

cryopreservation in Japan.” Congreso Internacional

Biotecnologia y Agricultura Bioveg 2005, Cuba, Feb.

(2005).

Kobayashi M., Abe H., Iuchi S., Kobayashi T.: “Report

on resource project in RIKEN BRC.” 16th International

Conference on Arabidopsis Research, Madison, Jun.

(2005).

Seki M., Ishida J., Iida K., Nakajima M., Enju A., Sakurai

T., Kamei A., Oono Y., Umezawa T., Fujita M., Mizukado

S., Morosawa T., Akiyama K., Narusaka Y., Narusaka

M., Go M., Kobayashi M., Kawai J., Hayashizaki Y.,

Shinozaki K.: “Expression profiling using Arabidopsis

whole-genome regulatory gene oligo DNA microarray

and production of Arabidopsis DNABook containing

about 1000 RAFL cDNAs for transcription factors.”

16th International Conference on Arabidopsis Research,

Madison, Jun. (2005).

1.

2.

3.

Umezawa T., Okamoto M., Kushiro T., Nambara E.,

Oono Y., Seki M., Koshiba T., Kobayashi M., Kamiya Y.,

Shinozaki K.: “CYP707A3, a major ABA 8'-hydroxylase

involved in dehydration and rehydration response in

Arabidopsis thaliana.” 3rd epso conference on Plant

dynamics: from Molecules to Ecosystems, Visegrad,

Hungary, May-Jun. (2006).

Yoshiki A., Kobayashi M., Nakamura Y., Yokoyama

K., Benno Y., Fukami K., Moriwaki K., Obata Y.: “The

Activities of the RIKEN BioResource Center.” 20th

IUBMB International Congress of Biochemistry and

Molecular Biology and 11th FAOBMB Congress, Kyoto,

Japan, Jun. (2006).

Kobayashi M., Abe H., Iuchi S., Kobayashi T.:

“Report on plant resource project in Riken BRC.” 17th

International Conference on Arabidopsis Research,

Madison, USA, Jun. (2006).

4.

5.

6.

【International Conference】

Experimental Plant DivisionRIKEN BRC Annual Report 2005 ～ 2007

― 56 ―

Iuchi S., Kobayashi M.: “Analysis of Arabidopsis

thaliana ecotypes under abiotic stress conditions.” 8th

International Congress of Plant Molecular Biology,

Adelaide, Australia, Sep. (2006).

Kobayashi M., Abe H., Iuchi S., Kobayashi T.: “Current

status of plant resource project in RIKEN BRC.” 18th

International Conference on Arabidopsis Research,

Beijing, China, Jun. (2007).

Iuchi S., Koyama H., Iuchi A., Kobayashi Y., Kitabayashi

S., Kobayashi Y., Ikka T., Hirayama T., Shinozaki K.,

Kobayashi M.: “Characterization of hypersensitive

mutant (stop1) to proton-rhizotoxicity.” 18th International

Conference on Arabidopsis Research, Beijing, China,

Jun. (2007).

Iuchi S., Suzuki H., Kim Y.-C., Iuchi A., Kuromori

T., Ueguchi M., Asami T., Yamaguchi I., Matsuoka

M., Nakajima M., Kobayashi M.: “Characterization

of knockout mutants for gibberellin receptor AtGID1s

in Arabidopsis thaliana".”International Plant Growth

Substances Association 19th Annual Meeting (19th

IPGSA Meeting), Puerto Vallarta, Mexico, Jul. (2007).

Nakajima M., Shimada A., Takashi Y., Kim Y.-C.,

Park S.-H., Ueguchi M., Suzuki H., Katoh E., Iuchi

S., Kobayashi Masatomo, Maeda T., Matsuoka M.,

Yamaguchi I.: “Characterization of Arabidopsis

gibberellin receptors.” International Plant Growth

Substances Association 19th Annual Meeting (19th

IPGSA Meeting), Puerto Vallarta, Mexico, Jul. (2007).

Abe H., Onishi J., Narusaka M., Seo S., Narusaka Y.,

Tsuda S., Kobayashi M.: “Analyses of plant response

to thrips feeding using Arabidopsis system.” 4th Asia-

Pacific Conference on Chemical Ecology, Tsukuba,

Japan, Sep. (2007).

7.

8.

9.

10.

11.

12.

【Domestic Conference】　Total 49