The UV-B stimulon of the terrestrial cyanobacterium Nostoc commune comprises early shock proteins and late acclimation proteins

Molecular Microbiology (2002)

46

(3), 827–843

© 2002 Blackwell Publishing Ltd

Blackwell Science, LtdOxford, UKMMIMolecular Microbiology0950-382XBlackwell Science, 200246Original Article

UV-B stimulon of Nostoc communeM. Ehling-Schulz et al.

Accepted 9 August, 2002. *For correspondence. E-mail [email protected]; Tel. (

+

49) 08161 713516; Fax (

+

49) 08161714512.

The UV-B stimulon of the terrestrial cyanobacterium

Nostoc commune

comprises early shock proteins and late acclimation proteins

Monika Ehling-Schulz,

1

Stefan Schulz,

2

Robin Wait,

3

Angelika Görg

4

and Siegfried Scherer

1

*

1

Microbial Ecology Group, Department of Biosciences, WZW, Technische Universität München, D-85354 Freising, Germany.

2

Stefan Schulz Datensysteme, D-81539 München, Germany.

3

KIR, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Hammersmith, London, UK.

4

Fachgebiet für Proteomik, Technische Universität München, D-85354 Freising, Germany.

Summary

The UV-B and desiccation-tolerant terrestrial cyano-bacterium

Nostoc commune

was grown underdefined UV irradiation. Proteome changes were mon-itored in the membrane and the cytosolic and theextracellular fractions. Tools were developed to sepa-rate stress-triggered from growth stage-dependentchanges. UV-B changed the relative cellular concen-tration of 493 out of 1350 protein spots at least by afactor of three, rendering the UV-B stimulon of

N.commune

the most complex one described so far.It comprises two different parts: an early shockresponse influencing 214 proteins and a late accli-mation response involving 279 proteins. The shockresponse comprised many membrane or membrane-associated proteins, whereas the acclimation re-sponse mainly changed cytosolic proteins. Most ofthe shock-induced changes were transient and didnot overlap with the acclimation response. In theextracellular fraction, UV irradiation induced superox-ide dismutase and the water stress protein. In total,27 intracellular, UV-B-induced proteins were partiallysequenced by electrospray ionization tandem massspectrometry. Three functional classes were identi-fied: proteins involved in lipid metabolism, in carbo-hydrate metabolism and in regulatory pathways.About 50% of the sequenced proteins were homolo-

gous to cyanobacterial database entries with un-known function. Interestingly, all of these proteinsbelong to the UV-B acclimation response. We con-clude that the UV-B shock response and the UV-Bacclimation response represent two completely dif-ferent and remarkably complex strategies of

N.commune

to protect itself against UV-B radiation inits natural environment.

Introduction

Cyanobacteria dominate the microbial communities ofsome of the most extreme environments on earth. Theyare often the primary colonizers of rock surfaces and soil(Whitton, 1987) and play an important role in preventingerosion and preserving water in the soil. It is therefore ofconsiderable importance to understand their adaptivestrategies towards changes of environmental conditions.One environmental factor which is receiving increasingattention is the rise of solar UV-B radiation reaching theearth’s surface due to the depletion of the stratosphericozone layer (Fraser

et al

., 1992). DNA, proteins and mem-branes are suggested to be important targets of detri-mental UV-B radiation (Tuveson

et al

., 1988; Barbato

et al

., 1995). However, to counteract UV damage, photo-synthetic microorganisms display a variety of mechanismswhich have been studied at the organismal and physio-logical level (for a review, see Ehling-Schulz and Scherer,1999).

In the terrestrial, highly UV-tolerant cyanobacterium

N.commune

, a cascade of physiological reactions wasobserved in response to UV-B. First, a rapid increase incarotenoids, especially echinenone and myxoxanthophyll,occurs. Second, an enormous increase of an extracellularUVA-/B-absorbing pigment that was associated with extra-cellular glycan synthesis was observed and, finally, scy-tonemin was slightly induced by UV-B and very stronglyby UV-A irradiation (Ehling-Schulz

et al

., 1997). The UVA-/B-absorbing pigment was shown to be an oligosaccha-ride mycosporine amino acid (OS-MAA), which is locatedin the extracellular glycan (Hill

et al

., 1994; Böhm

et al

.,1995). Several studies provide evidence that mycosporineamino acids (MAA) with absorption maxima between310 nm and 360 nm protect cyanobacteria and other

828

M. Ehling-Schulz

et al.

© 2002 Blackwell Publishing Ltd,

Molecular Microbiology

,

46

, 827–843

microorganisms by absorbing harmful UV radiation(Scherer

et al

., 1988; Karentz

et al

., 1991; Ehling-Schulz

et al

., 1997). MAAs are thought to originate from the firstpart of the shikimate pathway, but this hypothesis requiresadditional confirmation (Favre-Bonvin

et al

., 1987). Scy-tonemin, an extracellular pigment which has an

in vivo

absorption maximum at 370 nm, is known to function asa UV-A sunscreen in terrestrial cyanobacteria. It has beenshown that scytonemin synthesis requires

de novo

proteinsynthesis (Garcia-Pichel and Castenholz, 1991). The bio-chemical pathways that are involved in its synthesis areunknown.

Knowledge about the effects of UV radiation at thebiochemical and molecular level in cyanobacteria is verylimited. In the past, most studies focused on active repairmechanisms, such as DNA repair and turnover of the UV-sensitive D1 reaction centre protein of photosystem II(Eker

et al

., 1990; Campbell

et al

., 1998; Vass

et al

.,2000), but information about the global cellular responseupon prolonged UV irradiation is lacking. Nevertheless,based on SDS-PAGE data, it has been claimed that UV-B has almost no influence on the protein pattern of cyano-bacteria (Gerber and Häder, 1995; Masi and Melis, 1997;Chauhan

et al

., 1998).Proteome analysis, based on two-dimensional electro-

phoresis has developed into a powerful tool to investigateglobal changes in the gene expression programme oforganisms (VanBogelen

et al

., 1996; Antelmann

et al

.,1997; Godon

et al

., 1998). However, little information isavailable on the cyanobacterial proteome. The only pro-teome that has been studied in some detail is that of thelimnic

Synechocystis

sp. PCC 6803 (Sazuka and Ohara,1997; Sazuka

et al

., 1999), but no stress response studieshave been performed. In this study, we report on dramaticglobal changes of the

N. commune

proteome during UV

shock and UV acclimation, as is revealed by subtractivehigh-resolution two-dimensional gel electrophoresis(differential two-dimensional display). Subtractive pro-teome analysis allows one to correlate environmentaleffects with protein composition, but, in long-term experi-ments, the influence of growth on the proteome (growth-dependent proteome changes) also has to be taken intoaccount. To monitor the adaptation process over differentgrowth stages of

Nostoc

, a database application wasdeveloped and 27 UV-B-induced proteins were identifiedby mass spectrometry.

Results

Analysis of subcellular protein fractions

Nostoc commune

DRH1 cultures treated with UV andtheir corresponding control cultures grown without UVwere sampled under sterile conditions at intervals indi-cated in Fig. 1 and total cellular protein was isolated. Theprotein samples were fractionated before electrophoresisto get a better understanding of the location of proteinsinfluenced by UV-B. The cytosolic protein fraction wastested by immunostaining for contamination by waterstress protein Wsp. Wsp is an abundant protein in theextracellular glycan. None of the cytosolic water-solubleprotein fractions showed any signal in the immunoassay(data not shown). As expected, the membrane and cyto-solic protein fractions exhibited completely different two-dimensional patterns; the most abundant proteins of thecytosolic fraction are missing in the protein profile of themembrane fraction (Fig. 2). Because of the high extracel-lular polysaccharide content that disturbs isoelectricfocussing, two-dimensional electrophoresis turned out notto be an appropriate technique for analysis of the extra-

Fig. 1.

Growth curve of

Nostoc commune

DRH1 liquid cultures grown under nitrogen-fix-ing conditions at 30

∞

C receiving continuous light. For details of culture conditions, see Ehling-Schulz

et al

. (1997). Inset:

N. commune

DRH1 filament, grown 3 days with UV-B. Solid line, cultures exposed to UV-B (1.0 W m

-

2

); dashed line, cultures grown without UV-B; bars denote standard deviation of means; the thick arrow marks the beginning of UV-B irradiation; thin arrows mark time-points at which samples for two-dimensional electrophoresis were taken. Time-points that were sampled only in one experiment are indicated by white dots. EPS, extracellular polysaccharides; Hc, heterocyst.

UV-B stimulon of

Nostoc commune 829



,

46

, 827–843

Fig. 2

830

M. Ehling-Schulz

et al.



,

46

, 827–843

Fig. 2.

The UV-B stimulon of

N. commune

DRH1. Micropreparative two-dimensional electrophoresis gels of water-soluble cytosolic proteins (A, C) and membrane and membrane-associated proteins (B, D).A and B. UV-B shock response (3 h 1.0 W m

-

2

UV-B irradiation).C and D. UV-B acclimation response (3 days 1.0 W m

-

2

UV-B irradiation). Squares refer to sequenced proteins (see Table 2). Boxes at the margins provide parts of gel images of the corresponding control cultures grown without supplemented UV-B.

UV-B stimulon of

Nostoc commune 831



,

46

, 827–843

cellular proteins of

Nostoc

DRH1. Nevertheless, SDS-PAGE showed some influence of UV-B irradiation on theextracellular proteins, especially a fourfold increase of aprotein band of approximately 21 kDa (Fig. 3). Immuno-detection showed that UV-B also led to a fourfold inductionof the water stress protein Wsp, a 39 kDa polypeptide thatis only weakly stainable by silver (Scherer and Potts,1989).

Highly reproducible protein patterns were obtained forcytosolic and membrane fractions. In the cytosolic fractiona total of about 750 protein spots, and in the membranefraction, a total of about 600 proteins could be detectedreproducibly in the molecular mass range of 10 kDa to110 kDa and the pI range of pH 4–9.

Database application and statistical analysis

Development of a database application for Microsoft

ACCESS

provided the possibility to analyse the two para-meters, growth and stress, at the same time. A three-dimensional virtual master gel provided the possibility tomonitor the UV-B influence over different growth stages ofindividual spots, as well as global changes in gel profiles(for details, see

Experimental procedures

). Principal com-

ponent analysis (PCA) showed that the correspondingprotein fractions from different experiments are stronglycorrelated, whereas UV-treated gel profiles are clearlyseparated from their corresponding controls (Fig. 4). PCAis a common procedure to analyse complex datasets andhas already been used for proteome research previously

Fig. 3.

SDS-PAGE and Western blot analysis of extracellular proteins of

N. commune

DRH1.A. Proteins were analysed by SDS-PAGE after 12 h of UV-B irradia-tion (1.0 W m

-

2

). The gel was silver-stained.B. Western analysis using the Wsp antibody performed to test the influence of UV-B on the synthesis of Wsp, as Wsp remains non-stained by silver (Scherer and Potts, 1989).

+

UV-B, cultures exposed to UV-B; –UV-B, cultures grown without UV-B; Wsp, purified fraction of the water stress protein, a 39 kDa polypeptide; (

—

�

), indicates the position of the predominant band (approximately 21 kDa) induced by UV-B.

Fig. 4.

Principal component analysis (PCA) of corresponding gel profiles from two independent experiments demonstrates the repro-ducibility of the experimental procedure. Gel data are projected into a factorial subspace defined by the first two factors. The distance between gel profiles (indicated by points) within this space represents the degree of similarity between the gel profiles. The closer the gel profiles are located to the circle, the more of the variability is explained.A. Cytosolic fraction.B. Membrane fraction.UV-B, gel profile of a culture treated with supplemented UV-B (1.0 W m

-

2

); control, gel profile of a corresponding control culture grown without UV-B. E1 refers to the first experiment, E2 refers to a second experiment.

832

M. Ehling-Schulz

et al.



,

46

, 827–843

(e.g. Burstin

et al

., 1993; Vohradsky

et al

., 1997; Vasseur

et al

., 1999). PCA was performed to investigate the mainsources of variation in the gel profiles of protein fractionsfrom different growth and stress induction times (Fig. 5,for details on PCA see


). Thedifferences found in the gel profiles are explained statisti-cally by two factors. The first factor is the same for allprotein samples, whereas the second factor only affectedUV-B-treated samples. Long-time exposure experimentsusually include growth of the organism (Fig. 1). Thisresulted in significant time-dependent changes of the pro-teome that equally affected UV-B treated and control cul-tures (Fig. 5, factor 1). The first factor of the PCA thusreflected the growth-dependent changes in the proteomeof

N. commune

, whereas the second factor reflected theUV-B influence on the proteome.

UV-B stress influence on the proteome

Approximately 40% of all proteins detected by two-dimen-sional-electrophoresis were significantly affected by UV-B(Table 1), whereas the response at the proteome leveltowards UV-A irradiation and salt stress is far less complex

(M. Ehling-Schulz and S. Scherer, unpublished data). Thelatter results confirm that the UV-B response is indeedextremely complex. During the first 12 h of UV-B treat-ment, 108 spots of the cytosolic protein fractions and 123spots of the membrane fractions were influenced by UV-B. Most early reactions were transient; only 12 proteinspots of the cytosolic fractions and five protein spots ofthe membrane fractions were permanently changed. Afterprolonged UV-B treatment for 3 days, 162 spots of thecytosolic fractions and 100 spots of the membrane fractionshowed significant differences from the control fractions(Table 1). The influence of UV-B on protein synthesis canbe grouped in three categories: first, transient inductionor repression of proteins after short-term exposure (Fig. 6,type 1); second, durable induction or repression of pro-teins after short-term exposure (Fig. 6, type 2); and third,continuous increase or decrease of proteins after pro-longed exposure (Fig. 6, type 3).

Fig. 5.

PCA was performed using gel profiles of cytosolic protein fractions (A) and of membrane protein fractions (B). The first two factors cumulate 86% of the variability in case of the cytosolic frac-tions (A) and cumulate 88% of the variability in case of the membrane fractions (B). Triangles (

�

) indicate the first factor of PCA and squares (

�

) indicate the second factor of PCA. The solid lines indicate gel profiles of UV-B-treated cultures and the dashed lines indicate gel profiles of control cultures grown without UV-B.

Fig. 6.

The time-course of protein changes in response to UV-B is shown for selected proteins of

N. commune

DRH1. Solid lines, UV-B treated; dashed lines, control grown without UV-B.

UV-B stimulon of

Nostoc commune 833



,

46

, 827–843

Cytosolic water-soluble proteins showed differentkinetics in their response to UV-B irradiation comparedwith membrane bound-/associated proteins. The proteinresponse in the membrane fraction to UV-B was faster andstronger during early shock response than that of thecytosolic fraction (Fig. 5, Table 1). During shock response,27% of the analysed proteins in the membrane fractionchanged significantly, whereas in the cytosolic fractions18% of the analysed spots changed significantly. Spotsthat contributed to the UV-B triggered changes were dis-tributed over the entire proteome. The number of proteinsin the different fold categories were distributed over a widerange. The most frequent response was a more than 10-fold induction or repression, and newly synthesized pro-teins (Fig. 7). The majority of these proteins were low-abundance proteins with spot volumes (sum of theintensities of every pixel in the spot) below 100 (data notshown).

Identification of UV-induced proteins by ESI MS/MS

In total, 27 selected protein spots from the three differentcategories were partially sequenced by electrospray ion-ization tandem mass spectrometry (ESI MS/MS; Table 2).The resulting sequence tags showed an average identityof 97% to predicted gene products from the

Nostoc punc-tiforme

ATCC 29133 genome and an average identityof 84% to gene products predicted from the Anabaena(

Nostoc

) PCC 1720 genome sequence. For instance, oneof them, EC1, showed a 90% match to the biotin carbox-ylase from

Anabaena

PCC 7120, a subunit of the acetyl-CoA carboxylase (Gornicki

et al

., 1993) that catalyses thefirst step in long chain fatty acid biosynthesis. As thecorresponding genes of some of the sequenced proteinspots are clustered together in

Anabaena

and

N. puncti-forme

genomes, it is likely that these genes belong tostress regulated operons. Sequence tags from LC1 and

LC3 showed around 80% identity to two homologous geneproducts (BAB75749, BAB75750) in

Anabaena

, whosecoding sequences are located in the genome next to eachother and most probably belong to one operon.

As the genome of

N. commune

has not beensequenced, the corresponding genes were obtained fromthe genomic sequence of

N. punctiforme

. Three proteinsshowed no match to predicted protein sequences of

N.punctiforme

ATCC 29133 genome database or any other

Table 1.

Number of proteins from

Nostoc commune

DRH1 influenced by UV-B irradiation.

UV-B (1 W m

-

2

)

Water-solublecytosolic proteins

a

Membrane and membrane -associated proteins

a

+

b

-

b

+

b

-

b

Early transient reaction

c

25 71 33 85Early durable reaction

d

6 6 3 2Late reaction

e

71 91 50 50Total 102 168 86 137

a.

Proteins that are in the 68% interval of ln mean are omitted. Total number of proteins analysed: cytosolic protein fraction about 750; membraneprotein fraction about 600.b. +, new and increased proteins; –, absent and decreased proteins.c. Transient induction or repression of proteins after short-term exposure.d. Durable induction or repression after short time exposure;e. Continuous increase or decrease after prolonged exposure.

Fig. 7. Frequency plots of the protein spots that displayed a statisti-cally significant increase in response to UV-B relative to controls, according to their increase factors. Newly synthesized proteins are added to the >10-fold class.A. Cytosolic fractions.B. Membrane fractions.

834 M. Ehling-Schulz et al.

© 2002 Blackwell Publishing Ltd, Molecular Microbiology, 46, 827–843

Tab

le 2

. UV

-B-s

timul

ated

pro

tein

s id

entifi

ed b

y pr

otei

n se

quen

ce s

imila

rity.

Spo

t no

.A

min

o ac

id s

eque

nces

ded

uced

by E

SI

MS

/MS

ana

lysi

sTy

pe o

fre

actio

naIn

duct

ionb

kDa/

pHD

RH

1

Hom

olog

y to

Nos

toc

punc

tifor

me

ATC

C 2

9133

c

kDa/

pH

Hom

olog

y to

Ana

baen

a P

CC

7120

d,e

kDa/

pH

Put

ativ

e fu

nctio

n, id

entifi

edby

seq

uenc

e si

mila

rity

to d

atab

ase

entr

ies

Lipi

d m

etab

olis

mE

C1

ISG

YLP

PG

GP

GV

Rt

5 (1

2 h)

59C

ontig

394

gen

e 16

alr

0939

Bio

tin c

arbo

xyla

seLL

EE

AP

SLT

QE

QV

VLR

SY

LNIP

NIIA

AA

LTR

IDS

HV

YT

DY

QIP

PY

YD

SLI

GK

6.5

49/6

.1B

AB

7289

649

/6.3

LC2

VP

FAD

VG

LFK

l>1

0 (7

2 h)

43C

ontig

570

gen

e 8

alr0

897

Alc

ohol

deh

ydro

gena

seA

EV

LNY

EE

VG

6.5

43/6

.0B

AB

7285

443

/6.1

alr0

895

Bab

7285

243

/5.3

LC11

DF

SAT

SP

YAAY

DF

QE

PY

LRA

AH

PE

DA

LLAY

RT

IFG

TD

IQF

INA

NS

LNE

GD

AR

l8

(72

h)25

5.3

Con

tig 5

71 g

ene

2423

/5.2

all2

105

BA

B73

804

23/5

.3

Acy

l car

rier

prot

ein

phos

phod

iest

eras

e

LM2

VA

LLT

GA

DS

GLG

RG

SP

QLL

DY

SS

TK

l>1

0 (7

2 h)

406.

2C

ontig

650

, ge

ne 6

340

/9.3

alr5

182

BA

B76

881

31/5

.3

Sho

rt c

hain

deh

ydro

gena

se/

redu

ctas

e fa

mily

(SD

R-f

amily

)

Car

bohy

drat

e m

etab

olis

mE

M2

TAN

GE

AIA

QF

NR

VE

QV

LLP

IRD

GIT

LIR

t5

(12

h)33

4.6

Con

tig 5

51 g

ene

2231

/4.8

O-M

ethy

ltran

sfer

ase

LC9

ALD

LGV

NW

IDTA

AIY

GLG

HS

EE

VV

AK

VA

WT

LNH

NL[

GV

]LV

YS

P

l6

(72

h)38

5.4

Con

tig 5

97 g

ene

5435

.5/5

.3O

xido

redu

ctas

e/al

do/k

eto

redu

ctas

e fa

mily

LC12

DF

TE

VV

YR

SG

FAD

LYD

AR

TAIA

DE

HH

SF

LEK

l6

(72

h)22

4.2

Con

tig 6

51 g

ene

6520

/4.5

all3

586

BA

B75

285

18/4

.4

Tran

sald

olas

e si

gnat

ure

Reg

ulat

ory

path

way

sE

C5

LND

YLA

ED

Ht

3 (3

h)

235.

6C

ontig

626

gen

e 9

23/5

.6al

r123

8B

AB

7319

523

/5.6

Clip

P1

EM

1Y

LDE

PV

VV

DG

NLI

TS

RE

PG

DLP

IFT

TAIL

SR

tN

ew*

(12

h)43

5.9

Con

tig 6

26 g

ene

6740

/7.2

alr0

893

BA

B72

850

40/6

.6

Pro

teas

e

EM

5V

IGE

AA

NAT

QG

LKd

3 (2

4 h)

295.

8C

ontig

535

gen

e 6

26/6

.0al

r376

8B

AB

7546

726

/5.3

Two

com

pone

nt r

espo

nse

regu

lato

r

LM1

AE

AA

ALL

YQ

ALA

RQ

LNP

QQ

PLT

Rl

3 (7

2 h)

604.

4C

ontig

525

gen

e 8

59/4

.8al

r181

9B

AB

7351

858

/4.7

S-la

yer

prot

ein

sign

atur

e(S

LH d

omai

n)

a. t

, ea

rly t

rans

ient

rea

ctio

n; d

, ea

rly d

urab

le r

eact

ion;

l, la

te r

eact

ion

(see

Tab

le 1

).b

. Stim

ulat

ion

indi

ces

wer

e de

term

ined

in r

espo

nse

to 3

, 12,

24

and

72 h

UV-

B tr

eatm

ent.

The

hig

hest

val

ue w

as r

ecor

ded.

*N

ew r

efer

s to

pro

tein

spo

ts th

at w

ere

not d

etec

ted

in th

e co

rres

pond

ing

cont

rol g

els.

c. A

cces

s nu

mbe

r re

fers

to

the

prel

imin

ary

sequ

ence

of

N. p

unct

iform

e AT

CC

291

33 (

DO

E J

oint

Gen

ome

Inst

itute

).d

. A

cces

s nu

mbe

r re

fers

to

the

geno

mic

seq

uenc

e of

Ana

baen

a P

CC

712

0 (K

anek

o et

al.,

200

1); B

AB

num

ber

refe

rs t

o pr

otei

n en

try

at N

CB

I.e.

Thr

ee p

rote

ins

show

ed a

hig

h ho

mol

ogy

to m

ore

than

one

pro

tein

from

Ana

baen

a (N

osto

c) P

CC

712

0. S

eque

nce

tags

of L

C1

wer

e ho

mol

ogou

s to

BA

B75

749

(82%

iden

tity)

, BA

B75

750

(70%

iden

tity)

and

BA

B77

014

(61%

iden

tity)

; LC

2, B

AB

7285

4 (9

5% id

entit

y) a

nd B

AB

7285

2 (8

5% id

entit

y); L

C3,

BA

B75

750

(78%

iden

tity)

, B

AB

7574

9 (6

1% id

entit

y) a

nd B

AB

7701

4 (5

6% id

entit

y).

UV-B stimulon of Nostoc commune 835


Unk

now

n fu

nctio

n

EC

2V

TPA

DA

GTA

DQ

RV

VD

QD

TV

ET

QK

QA

LDY

DY

EE

RE

ELD

VN

SG

NLP

IEE

d7

(12

h)48

4.5

Con

tig 5

98 g

ene

834

/4.5

all4

050

BA

B75

749

37/5

.0al

l405

1B

AB

7575

033

/4.7

all5

315

BA

B77

014

34/4

.8

EC

4IG

DV

VS

DA

VY

SD

GS

FK

d6

(24

h)28

5.5

Con

tig 6

11 g

ene

728

/5.4

EM

3D

AV

SA

VIE

NF

QE

KS

AV

SQ

VG

SE

FK

QG

SS

ELR

EK

IQA

DLQ

QA

K

dN

ew*

(24

h)31

6.1

Con

tig 4

33 g

ene

130

/5.3

alr0

162

BA

B77

686

30/5

.1YA

QLQ

AQ

LAIV

R

LC1

QA

LDY

DY

EE

RR

EE

LDV

NS

GN

LPIE

ER

LED

FE

PN

YR

d7

(12

h)48

4.5

Con

tig 5

98 g

ene

834

/4.5

all4

050

BA

B75

749

37/5

.0al

l405

1B

AB

7575

033

/4.7

all5

315

BA

B77

014

34/4

.8

LC3

SLV

LYT

EG

GD

RE

LVY

EE

Tl

6 (2

4 h)

424.

7C

ontig

598

gen

e 7

37/5

.1al

l405

1B

AB

7575

033

/4.7

all4

050

BA

B75

749

37/5

.0al

l531

5B

AB

7701

434

/4.8

LC4

KN

VT

QF

IEK

GS

ELS

LYE

KV

GA

DV

LLA

IGP

LNT

INF

EN

RE

FT

GQ

DA

DQ

GIW

AR

SD

LNIQ

DV

IRIQ

EY

FG

QIY

K

lN

ew*

(72

h)39

4.9

Con

tig 5

26 g

ene

739

/5.2

alr3

199

BA

B74

898

40/5

.2

Spo

t no

.A

min

o ac

id s

eque

nces

ded

uced

by E

SI

MS

/MS

ana

lysi

sTy

pe o

fre

actio

naIn

duct

ionb

kDa/

pHD

RH

1

Hom

olog

y to

Nos

toc

punc

tifor

me

ATC

C 2

9133

c

kDa/

pH

Hom

olog

y to

Ana

baen

a P

CC

7120

d,e

kDa/

pH

Put

ativ

e fu

nctio

n, id

entifi

edby

seq

uenc

e si

mila

rity

to d

atab

ase

entr

ies

a. t

, ea

rly t

rans

ient

rea

ctio

n; d

, ea

rly d

urab

le r

eact

ion;

l, la

te r

eact

ion

(see

Tab

le 1

).b

. Stim

ulat

ion

indi

ces

wer

e de

term

ined

in r

espo

nse

to 3

, 12,

24

and

72 h

UV-

B tr

eatm

ent.

The

hig

hest

val

ue w

as r

ecor

ded.

*N

ew r

efer

s to

pro

tein

spo

ts th

at w

ere

not d

etec

ted

in th

e co

rres

pond

ing

cont

rol g

els.

c. A

cces

s nu

mbe

r re

fers

to

the

prel

imin

ary

sequ

ence

of

N. p

unct

iform

e AT

CC

291

33 (

DO

E J

oint

Gen

ome

Inst

itute

).d

. A

cces

s nu

mbe

r re

fers

to

the

geno

mic

seq

uenc

e of

Ana

baen

a P

CC

712

0 (K

anek

o et

al.,

200

1); B

AB

num

ber

refe

rs t

o pr

otei

n en

try

at N

CB

I.e.

Thr

ee p

rote

ins

show

ed a

hig

h ho

mol

ogy

to m

ore

than

one

pro

tein

from

Ana

baen

a (N

osto

c) P

CC

712

0. S

eque

nce

tags

of L

C1

wer

e ho

mol

ogou

s to

BA

B75

749

(82%

iden

tity)

, BA

B75

750

(70%

iden

tity)

and

BA

B77

014

(61%

iden

tity)

; LC

2, B

AB

7285

4 (9

5% id

entit

y) a

nd B

AB

7285

2 (8

5% id

entit

y); L

C3,

BA

B75

750

(78%

iden

tity)

, B

AB

7574

9 (6

1% id

entit

y) a

nd B

AB

7701

4 (5

6% id

entit

y).

Tab

le 2

.co

nt.



LC5

ALQ

QLV

LEN

ER

VG

AD

VLL

AIG

PLN

TIN

FE

NR

VQ

DA

MA

AV

SG

VV

GS

AV

TQ

TS

DK

VN

TLF

TE

LLQ

SD

NP

QK

DLT

AH

AE

AE

EE

VV

PN

NLS

SD

QS

EQ

LAT

EF

K

l>1

0 (7

2 h)

395.

2C

ontig

526

gen

e 7

39/5

.2al

r319

9B

AB

7489

840

/5.2

LC6

ALQ

QLV

LEN

ER

VG

AD

VLL

AIG

PLN

TIN

FE

NR

EF

TG

QD

AD

QG

IWA

RS

DLN

IQD

VIR

LDH

NK

VN

TLF

TE

LLQ

SD

NP

QK

IQE

YF

GQ

IYK

DLT

AH

AE

AE

EE

VV

YP

R

lN

ew*

(72

h)39

5.2

Con

tig 5

26 g

ene

739

/5.2

alr3

199

BA

B74

898

40/5

.2

LC7

ALQ

QLV

LEN

ER

VN

TLF

TE

LLQ

SD

NP

QK

IQE

YF

GQ

IYK

lN

ew*

(72

h)39

5.25

Con

tig 5

26 g

ene

739

/5.2

alr3

199

BA

B74

898

40/5

.2

LC8

YY

LLE

QE

HG

YY

[AF

]QLE

DF

GA

EY

FQ

VY

PV

LLF

PT

DY

IEP

GT

DE

KN

TFA

TS

AYIA

TS

PE

SA

FE

YLC

SLK

EQ

IDE

DT

WLG

TAS

GY

HK

lN

ew*

(72

h)40

6.2

Con

tig 3

64 g

ene

437

/5.5

all0

425

BA

B72

383

38/5

.5

LC10

AQ

EA

LGLN

QP

IKV

EK

LFG

EE

PE

QQ

IGD

ELR

lN

ew*

(72

h)30

5.1

Con

tig 6

26 g

ene

6825

/5.0

alr0

894

BA

B72

851

26/5

.9

LM3

YAQ

LQA

QLA

IVR

EK

IQA

DLQ

QA

KD

AV

SA

VIE

NF

QE

K

dN

ew*

(24

h)30

6.1

Con

tig 4

33 g

ene

130

/5.3

alr0

162

BA

B77

686

30/5

.1

LM4

NK

FV

SG

LIG

GE

GLF

QT

KT

ST

LNY

RV

EK

l7

(24

h)29

.5 6.4

Con

tig 5

73 g

ene

824

/7.7

No

hom

olog

ies

foun

d in

dat

abas

e en

trie

sE

C3

[VA

]LC

LGAY

MG

VR

t3

(3 h

)35

5.0

EM

4T

GT

TT

YS

GE

GD

MA

Pt

3 (3

h)

29.5 6.15

EM

6Y

SY

LNN

AG

EA

NS

Lt

New

* (1

2 h)

215.

6

Spo

t no

.A

min

o ac

id s

eque

nces

ded

uced

by E

SI

MS

/MS

ana

lysi

sTy

pe o

fre

actio

naIn

duct

ionb

kDa/

pHD

RH

1

Hom

olog

y to

Nos

toc

punc

tifor

me

ATC

C 2

9133

c

kDa/

pH

Hom

olog

y to

Ana

baen

a P

CC

7120

d,e

kDa/

pH

Put

ativ

e fu

nctio

n, id

entifi

edby

seq

uenc

e si

mila

rity

to d

atab

ase

entr

ies

a. t

, ea

rly t

rans

ient

rea

ctio

n; d

, ea

rly d

urab

le r

eact

ion;

l, la

te r

eact

ion

(see

Tab

le 1

).b

. Stim

ulat

ion

indi

ces

wer

e de

term

ined

in r

espo

nse

to 3

, 12,

24

and

72 h

UV-

B tr

eatm

ent.

The

hig

hest

val

ue w

as r

ecor

ded.

*N

ew r

efer

s to

pro

tein

spo

ts th

at w

ere

not d

etec

ted

in th

e co

rres

pond

ing

cont

rol g

els.

c. A

cces

s nu

mbe

r re

fers

to

the

prel

imin

ary

sequ

ence

of

N. p

unct

iform

e AT

CC

291

33 (

DO

E J

oint

Gen

ome

Inst

itute

).d

. A

cces

s nu

mbe

r re

fers

to

the

geno

mic

seq

uenc

e of

Ana

baen

a P

CC

712

0 (K

anek

o et

al.,

200

1); B

AB

num

ber

refe

rs t

o pr

otei

n en

try

at N

CB

I.e.

Thr

ee p

rote

ins

show

ed a

hig

h ho

mol

ogy

to m

ore

than

one

pro

tein

from

Ana

baen

a (N

osto

c) P

CC

712

0. S

eque

nce

tags

of L

C1

wer

e ho

mol

ogou

s to

BA

B75

749

(82%

iden

tity)

, BA

B75

750

(70%

iden

tity)

and

BA

B77

014

(61%

iden

tity)

; LC

2, B

AB

7285

4 (9

5% id

entit

y) a

nd B

AB

7285

2 (8

5% id

entit

y); L

C3,

BA

B75

750

(78%

iden

tity)

, B

AB

7574

9 (6

1% id

entit

y) a

nd B

AB

7701

4 (5

6% id

entit

y).

Tab

le 2

.co

nt.



bacterial sequences in protein databases. Besides thestriking homologies to closely related cyanobacterial spe-cies (belonging to the family Nostocaceae/section IV ofcyanobacteria), for several proteins a significant homologyto gene products from Deinococcus radiodurans wasobserved. Only low homologies (in most cases none orbelow 30%) to Synochocystis sp. PCC 6803, whichbelongs to section II of cyanobacteria, were found (datanot shown). Eleven proteins spots were tentatively identi-fied by sequence similarities. For 13 protein spots, only ahomology to hypothetical proteins of N. punctiforme ATCC29133 and Anabaena (Nostoc) PCC 1720 with unknownfunction was found, or homologies to conserved hypo-thetical proteins from the highly desiccation and radiation-resistant bacterium Deinococcus radiodurans wereobserved.

Discussion

Influence of UV-B on extracellular proteins

Recently, it was reported that in the isolated extracellularglycan of N. commune DRH1, UV-B irradiation generatedsuperoxide radicals that were scavenged by a superoxidedismutase (SOD) located within the glycan (Shirkey et al.,2000). We observed in our approach, using the samestrain, a protein of the same molecular weight from theextracellular protein fraction that was strongly induced byUV-B. As SDS-PAGE of extracellular proteins of N. com-mune DRH1 showed only very few, but clearly resolvedbands (Fig. 3), this protein most probably is SOD. SODmutants of the highly radiation resistant D. radioduranswere reported to be more sensitive to ionizing radiationthan the wild type (Markillie et al., 1999). The induction ofmycosporine (MAA) synthesis is associated with theinduction of a water stress protein (Wsp, Scherer andPotts, 1989), supporting the role of the latter in the syn-thesis of the oligosaccharide-MAA which has been pro-posed by Hill et al. (1994). Wsp is clearly induced byUV-B by a factor of four (Fig. 3). However, further studiesare necessary to unravel its specific role, i.e. whether if itis directly involved in the synthesis of oligosaccharide-MAA or in modification of the glycan to provide a matrixfor oligosaccharide-MAA.

Influence of UV-B on the proteome

There are only few studies dealing with the UV-B stressresponse of cyanobacteria. An ATP-dependent Clp pro-tease (ClpP1) isolated from Synechococcus sp. PCC7942 was UV-B and cold inducible (Porankiewicz et al.,1998). It has been claimed by several authors that UV-Bhas very little influence on the protein pattern of cyano-bacteria (Gerber and Häder, 1995; Masi and Melis, 1997;

Chauhan et al., 1998). The latter studies are based onone-dimensional SDS-PAGE analysis. However, SDS-PAGE may not be suitable to monitor the UV acclimationprocess at the proteome level, as its resolution is far toolow (e.g. Ehling-Schulz and Scherer, 1999). To our knowl-edge, no proteome studies reporting on the UV-B stimulonof cyanobacteria are available. In general, any detailedglobal analysis of protein synthesis under specific envi-ronmental conditions to define stimulons is missing forcyanobacteria. The term stimulon refers to a set of pro-teins whose amount or synthesis rate changes inresponse to a specific environmental stimulus (Smith andNeidhardt, 1983).

First of all, the UV-B response turned out to be surpris-ingly complex. Semiquantitative analysis of about 1350proteins revealed that at least 493 proteins (37%) belongto the UV-B stimulon. A minimum of 188 proteins werepositively stimulated, whereas a minimum of 305 proteinswere negatively affected (Table 1). The relative decreaseof proteins in stressed cells could be due to the repressionof their synthesis, but could also be the result of a differ-ential turnover. This cannot be decided based on the dataavailable. In Saccharomyces cerevisiae, the synthesis of115 proteins was stimulated by H2O2, whereas 52 otherproteins were repressed. Except for a few targets, theH2O2 response was transient (Godon et al., 1998). InEscherichia coli, Salmonella typhimurium and Bacillussubtilis, different types of stimulons have been described(Spector et al., 1986; VanBogelen et al., 1996; Antelmannet al., 1997). The phosphate limitation (PL) stimulon in E.coli included 315 proteins when a factor of three in spotintensity change is used as a significance limit. Half ofthese proteins were positively affected and half of themwere negatively affected (VanBogelen et al., 1996). Thetotal of 493 proteins changing in response to UV-B makethe UV-B stimulon the most complex one described so far.Importantly, these changes are the result of true adapta-tion and not of damage, as no growth delay was observedin N. commune (Ehling-Schulz et al., 1997).

Identification of UV-B-induced proteins

Partial sequences of a set of UV-B stimulated proteinsshowed that these can be grouped into three functionalclasses (Table 2): first, proteins involved in lipid metabo-lism; second, proteins involved in carbohydrate metabo-lism; and third, proteins with regulatory function. Therewas a group of proteins with unknown function and threeproteins which showed no homology to any databaseentries at all. Interestingly, all sequenced proteins thatwere homologous to cyanobacterial gene products withunknown function belonged to the UV-B acclimationresponse. To these unknown genes, the phenotype ‘UV-induced’ is now associated.



Four proteins were identified, which are thought to beinvolved in lipid metabolism. In microalgae and diatoms,alterations in lipid and fatty acid composition were ob-served in response to UV-B (Döhler and Biermann, 1994;Wang and Chai, 1994). As membranes are main targetsof UV-B induced damage (Hideg and Vass, 1996; seeTable 1) and fatty acid composition plays a crucial role inmembrane fluidity (Kaneda, 1991), fatty acid compositionin N. commune is predicted to change to counteract UV-B damage.

Three of the proteins identified were homologues toproteins that are involved in carbohydrate metabolism.Carbohydrate metabolism is suggested to play a key rolein UV-B stress tolerance of N. commune, as it was shownthat this organism counteracts UV-B stress by synthesisof extracellular polysaccharides (EPS) and the produc-tion of UV-B absorbing oligosaccharide mycosporines(Ehling-Schulz et al., 1997). The physical properties of theEPS change in response to UV-B (data not shown) and itwas recently suggested that polysaccharide structure ofN. commune could be modified in response to environ-mental changes (Helm et al., 2000).

The number of proteins directly contributing to UV-Btolerance is currently unknown as an alteration in the levelof expression in response to UV-B treatment does notnecessarily imply a role in UV-B tolerance and is likely tobe the result of indirect secondary effects. Some of theproteins induced by UV-B are also salt inducible; there-fore, the UV-B stimulon most probably also comprisesgeneral stress proteins, for example, LC9 showed signifi-cant homology to Gsp69, a general stress protein of B.subtilis (Antelmann et al., 1997). Two proteins with homol-ogies to proteases were found. The corresponding geneof one of them showed 77% identity to the Clp proteaseproteolytic subunit 1 (ClpP1) from Synechococcus sp.PCC 7942, which is essential for UV-B acclimation ofSynechococcus (Porankiewicz et al., 1998). The se-quence tag obtained from the other one, EM5, a proteinwhich was also salt inducible (M. Ehling-Schulz and S.Scherer, unpublished), showed a 100% match to the twocomponent response regulator OrrA from AnabaenaPCC7120, which belongs to the LuxR family of bacterialregulatory proteins and was shown to regulate anosmotic-responsive gene (Schwartz et al., 1998).

UV-stress-induced gene duplication and post-translational modification?

Some of the sequenced proteins that belong to the UV-Bstimulon of N. commune DRH1 were significantly homol-ogous to more than one gene product predicted from thegenome of Anabaena (Nostoc) PCC7120 and the genomeof N. punctiforme ATCC 29133 (see Table 2). Because ofthe high homology of sequence tags from LC1 and LC3

to two homologous gene products in Anabaena, whosecorresponding coding sequences are located in thegenome next to each other, it is suggested that they arethe result of tandem gene duplication. Recently, it wasreported from the highly radiation-resistant D. radioduransthat gene duplication plays a significant role in its stresstolerance (White et al., 1999; Makarova et al., 2001). Onthe other hand, four UV-B acclimation proteins (LC4-LC7,Fig. 2) have been identified that are suggested to repre-sent isoforms due to UV-B induced post-translationalmodifications. In control cultures only low amounts of asingle protein spot were detected. Besides of putativephosphorylation sites, two putative glycosylation siteswere predicted from sequence analysis of the correspond-ing protein. A high rate of post-translational modificationswas reported from cyanobacteria (Sazuka et al., 1999) butthe physiological significance of these post-translationalmodifications is not known.

UV-B shock response versus UV-B acclimation response

The stress response of a bacterial cell following anenvironmental signal can be divided into a shock re-sponse and an acclimation response (Panoff et al., 1997).Although it is difficult to delineate the difference betweenthese responses, we propose to term a transient responsetowards an external stimulus a ‘shock response’, whereasa stable change is termed ‘acclimation response’. The UV-B stimulon of N. commune clearly comprises two differentsets of proteins: an early shock response of 214 proteins,occurring within the first 12 h, and a late acclimationresponse of 279 proteins, which requires from1 up to3 days.

Shock proteins are sometimes bulk proteins, for exam-ple, the major cold shock protein CspA of E. coli accountsfor 13% of total cellular protein 1 h after cold shock(Goldstein et al., 1990). No bulk proteins were observedin N. commune after UV-B shock. Several proteins wereinduced or repressed more than 10-fold or newly synthe-sized (Fig. 7), but most of them were low abundance pro-teins with volumes below 0.4% of total cellular proteins(data not shown). In N. commune, most of the proteinchanges observed during shock response were transient(Table 1). This finding is consistent with physiologicaldata: UV-B irradiation of N. commune led to a rapid, buttransient increase of outer membrane-bound carotenoidsand a delayed but permanent increase of glycan and MAAsynthesis. It has been proposed that the outer membrane-bound carotenoids provide a fast, active response tocounteract acute cell damage (Ehling-Schulz et al., 1997).Furthermore, the response to UV-B on the protein expres-sion profile of the membrane was faster than that on thecytosolic protein expression profile (Fig. 5, factor 2) andthe protein composition of the membrane fraction was



more strongly influenced during shock response (Table 1).In contrast, the cytosolic protein fraction was morestrongly influenced by prolonged UV-B exposure than wasthe membrane fraction. As membranes are known to beprimary targets for UV-B induced damage by reactiveoxygen intermediates and free radicals (Tuveson et al.,1988; Hideg and Vass, 1996), we conclude that the mem-brane composition is a major, although not the only, targetof the UV shock response.

It was a surprising observation that the transient UV-Bshock response has nearly no overlap with the later UV-B acclimation response. After causing a transient‘emergency reaction’, UV-B switches the cellular activitytowards long-term protective functions and we assumethat the majority of the stimulated proteins is needed forcontinuous growth under UV-B stress. Long-term UV-Bexposure of N. commune led to a decreased cell numberbut increased dry weight in comparison to control cultures,whereas short-term UV-B exposure had negligible effectson the growth of N. commune. It has been proposed thatthe reduction of cell replication is caused by the metaboliccost of massive extracellular glycan synthesis and sun-screen production (Ehling-Schulz et al., 1997).

In summary, we conclude that the UV-B shock responseand the UV-B acclimation response of N. commune rep-resent two remarkably complex, but completely differentstrategies of this organism to protect itself against UV-Bradiation. However, we have just started to unravel theexceedingly complex mechanisms of UV-B protection ofthis organism.


Organism, growth conditions and growth measurement

The cyanobacterium N. commune Vauch. strain DRH 1 wasderived from field material of N. commune collected in theHunan province, China (Hill et al., 1994). For UV inductionexperiments, N. commune DRH 1 liquid cultures were grownunder nitrogen-fixing conditions at 30∞C as described previ-ously (Ehling-Schulz et al., 1997). Visible light was obtainedfrom a cool white fluorescent tube (L 40 W/25 S, Osram,approximately 2.4 W m-2). Additional UV-illumination wasprovided by a Philips TL 40 W/12 lamp with an incidentirradiance of 100–140 mW m-2 nm-1 at 310 nm, and 50–70 mW m-2 nm-1 at 330 nm. UV-A experiments were per-formed using a Philips TL 36 W/08 lamp with an emissionmaximum centred at 375 nm. The spectral irradiance whichwas received by the cultures has been described in detailpreviously (Ehling-Schulz et al., 1997). Because chlorophylla content per cell remained unaffected, even after prolongedexposure to UV-B, while total dry weight was rising (Ehling-Schulz et al., 1997), growth curves were calculated fromchlorophyll a spectra (1.4 ± 0.2 mg of chlorophyll a corre-sponds to 107 cells). Chlorophyll a contents were determinedas described previously (Ehling-Schulz et al., 1997). Cultures

were precultivated for 2.5 days; thereafter UV irradiation wasprovided.

Preparation of protein fractions

Cultures treated with UV and their corresponding controlcultures grown without UV were sampled under sterileconditions at indicated intervals in Fig. 1. Cultures were har-vested by centrifugation and cells were washed three timeswith Tris-HCl pH 7.8 (10 mM, 30∞C) to remove extracellularpolysaccharides and proteins. Supernatants were concen-trated by ultrafiltration (Centricon, 10 kDa cut-off, Amicon)and speedvac evaporation. This fraction contained the extra-cellular proteins. The extracellular protein fractions weretested to be free of intracellular proteins by spectrophoto-metry (excitation spectra, excitation 355 nm) to detect phy-cobiliproteins, which are the most abundant proteins incyanobacterial cells. After the last washing step, cells wereresuspended in Tris-HCl pH 7.8. Proteinase inhibitor Pefabloc(0.1 mM; Boehringer Mannheim) was added and the suspen-sion was pasred twice through a precooled French pressurecell (SLM AMINCO) at 140 MPa. Cell debris was removed byultracentrifugation at 100 000 g for 1 h at 15∞C. The efficiencyof the removal of extracellular proteins was tested by immu-noblotting according to Hill et al. (1994). To the supernatantfraction, which contained the intracellular water-soluble pro-teins (‘cytosolic protein fraction’), the following substanceswere added (final concentrations): 8 M urea, 2% 3-[(3-cholamidopropyl) -di-methylammonio]-1-propane-sulphonate(CHAPS), 1% 1,4-dithiothreitol (DTT) and 0.8% Pharmalyte3–10 (Amersham-Pharmacia Biotech) and the samples werestored in aliquots at -70∞C until analysed.

The 100 000 g pellet was washed with Tris-HCl pH 7.8(15∞C, 100 000 g, 30 min), resuspended in a detergent buffercontaining 8 M urea, 2% CHAPS, 1% DTT and 0.8% Phar-malyte 3–10 (Amersham-Pharmacia Biotech) and sonicatedthree times for 10 s each in an ice-water bath using aSoooplus microtip sonicator (Bandelin). Samples were thencentrifuged (15∞C, 8000 g, 30 min). The supernatant fraction,containing membrane bound and membrane-associated pro-teins (‘membrane protein fraction’), was centrifuged again(15∞C, 8000 g, 15 min), recovered and stored at -70∞C untilanalysis.

SDS-PAGE and Western analysis

SDS-PAGE was performed on 15% (w/v) polyacrylamide gelsin a discontinuous buffer system according to Laemmli(1970). Western blot analysis was performed using a Wspantibody according to Hill et al. (1994). For detection, the BMchemiluminescence Western blotting kit from BoehringerMannheim was used.

High resolution two-dimensional gel electrophoresis

Two-dimensional electrophoresis was performed with immo-bilized pH gradients in the first dimension and SDS-PAGE inthe second dimension (IPG-Dalt) according to Görg et al.(2000). For analytical purposes, isoelectric focusing was car-ried out on IPG 4–9 gel strips, which had been rehydrated in



8 M urea, 0.5% CHAPS, 0.2% DTT, 0.2% Pharmalyte 3–10overnight. Each IPG strip was loaded with approximately60 mg of protein, using the Immobiline Dry-Strip Kit (Amer-sham-Pharmacia Biotech) and focused for 16 000 Vh at 20∞Cunder oil. For microseparation, IPG 4–7 gel strips, loadedwith approximately 200 mg protein, were used. Before thesecond dimension, strips were equilibrated for 2 ¥ 15 min inTris-HCl, pH 8.8 (50 mM), containing 6 M urea and 30% glyc-erol. Then, 1% DTT was added to the first equilibration stepand 4.8% iodoacetamide was added to the second equilibra-tion step. SDS-PAGE was carried out in 13% (w/v) poly-acrylamide gels. For analytical purposes, UV-treated andcorresponding control cultures were focused together, runon the same second dimension SDS-PAGE and stainedtogether. For micropreparation, multiple SDS-PAGE was per-formed on a vertical system as described (Görg et al., 2000).

Resolved polypeptides were silver-stained according toBlum et al. (1987) or, in the case of peptide sequencing,according to Shevchenko et al. (1996). No differentiation wasmade between ‘novel’ and ‘increased’ proteins, as proteinsthat were often stated to be ‘novel’ may just be expressed inthe control below the detection limit of the staining methodused. It has been stated that almost all proteins of a cell areexpressed constitutionally in low copy number by replication-induced protein synthesis (RIPS; for a review see Humphery-Smith, 1999).

Protein digestion for mass spectrometry

Selected protein spots were cut from silver-stained gels andin-gel digestion with trypsin was performed according to pub-lished methods (Shevchenko et al., 1996; Wilm et al., 1996)modified for use with a robotic digestion system (Wait et al.,2001) (Investigator ProGest). Briefly, silver-stained gel pieceswere first washed with 30 ml of 15 mM potassium ferricya-nide/50 mM sodium thiosulphate (Gharahdaghi et al., 1999),followed by three rinses with 100 ml deionized water. Cysteineresidues were reduced with DTT and derivatized by treat-ment with iodoacetamide. The gel pieces were then dehy-drated with acetonitrile and dried at 60∞C, before addition ofmodified trypsin (Promega); 10 ml at 6.5 ng ml-1 in 25 mMammonium hydrogen carbonate. After incubation at 37∞C for8 h, the products were recovered by sequential extractionswith 25 mM ammonium hydrogen carbonate, 5% formic acidand acetonitrile. Extracts were lyophilized and resuspendedin 7 ml of 0.1% formic acid for analysis by tandem electro-spray mass spectrometry (ESI MS/MS).

HPLC ESI MS/MS

Tandem electrospray mass spectra were recorded using ahybrid quadruple/orthogonal acceleration time of flight spec-trometer (Q-Tof; Micromass) interfaced to a MicromassCapLC capillary chromatograph. Then, 1.4 ml aliquots of eachsample were injected onto an 300-mm ¥ 15 mm desaltingcolumn, packed with Pepmap C18 (LC Packings), andwashed for 3 min with 0.1% aqueous formic acid (with thestream select valve diverting the column effluent to waste).The flow rate was then reduced to 1 ml per min, the streamselect valve was switched to the data acquisition position,

and an acetonitrile/0.1% formic acid gradient (5% to 70%acetonitrile over 20 min) was initiated to elute peptides intothe mass spectrometer. The capillary voltage was set to3500 V, and data-dependent MS/MS acquisitions were per-formed on precursors with charge states of 2, 3 or 4 over asurvey mass range 540–1000. Known trypsin autolysis prod-ucts and keratin-derived precursor ions were automaticallyexcluded. The collision gas was argon, and the collision volt-age was varied between 18 V and 45 V, depending on thecharge state and mass of the precursor. Daughter ion spectrawere charge-state de-encrypted and de-isotoped with a max-imum entropy algorithm (MaxEnt 3, Micromass), and uninter-preted mass spectra were correlated to entries in the N.punctiforme ATCC 29133 protein database, using PROTEIN

LYNX global server (Version 1; Micromass). In cases wheredirect matching of the tandem mass spectra failed toretrieve any hits, amino acid sequences were deducedsemimanually from the spectra with the assistance ofMicromass’s peptide sequencing program, PEPSEQ. The re-sulting sequences were searched against the N. punctiformeATCC 29133 genome, and against NCBI’s non-redundantdatabase using BLAST (Altschul et al., 1997). The N. punc-tiforme ATCC 29133 genome data were obtained from theDOE Joint Genome Institute (JGI) at http://www.jgi.doe.gov/JGI_microbial/html/nostoc/nostoc_homepage.html. The Ana-baena PCC 1720 genome data were obtained from Cyano-Base at http://www.kazusa.or.jp/cyanbase/ (Kaneko et al.2001).

Image data analysis

Computer-assisted image analysis was used for spot detec-tion and volume measurement. The volume of a spot isdefined as the sum of the intensities of every pixel in the spot.It can be viewed as a measure of the three-dimensional sizeof the spot, in which intensity is the third dimension (IMAGE-

MASTER 2D ELITE version 2, Amersham-Pharmacia Biotech).pIs were calculated from the pH gradient of the focused IPGstrips and molecular weights were estimated from proteinstandards that co-migrated in the second dimension. Repro-ducibility of the two-dimensional analysis was tested by run-ning the same sample twice on independent gels, andreproducibility of the growth experiments was tested by prin-cipal component analysis (PCA). Principal component anal-ysis is a multivariate technique in which a number of relatedvariables is transformed to smaller sets of uncorrelated vari-ables, the principal components. These variables are orderedso that the first few (principal components) retain most of thevariation present in all of the original variables (Jolliffe, 1986).One of the advantages of PCA is that n-dimensional data canbe projected on a two-dimensional plot while most of thevariability is saved. General description of principal com-ponent analysis can be obtained from the National Instituteof Standards and Technology (NIST): NIST/SEMATECHEngineering Statistics Internet Handbook: http://www.itl.nist.gov/div898/handbook/index.htm. The ‘cumulative percent-age’ calculated from the eigenvalues give an idea of theglobal variability that is represented. In general, the variabilityof a dataset is statistical sufficiently explained by the factorsthat cumulate 70% of total variability (Jolliffe, 1986). A totalof about 100 gels has been run during this approach and a

http://www.jgi.doe.gov/

http://www.kazusa.or.jp/cyanbase/

http://www.itl.nist



subset of 46 gels has been analysed quantitatively by com-puter-assisted image analysis. Subtractive gel comparisonwas performed at different time-points. Gels were matchedin a two-step procedure. In the first step, gel images of stresstreated and their corresponding control cells were matched.In a second step, gel images of the different time-points werematched to provide the possibility to follow the changes ofindividual spots over time. All gels were matched to eachother. A database application for Microsoft ACCESS was devel-oped to generate a three-dimensional virtual master gel thatfacilitated the monitoring of the UV adaptation process overdifferent growth stages of N. commune. The mean of the log-normal distribution of spot volumes (ln mean) was used asnormalization variable as it is independent of the number ofspots in a gel and the stain variability from protein to protein(Burstin et al., 1993; Vohradsky et al., 1997). Spots with avolume smaller than 0.15, or an area smaller than 200 pixels,or a density (volume/area) lower than 0.018, were discarded(Garrels, 1989). Spots that were outside the 68% interval ofln mean were considered to be significantly changed. The68% interval is defined by the median ± standard deviation,which corresponds to a factor of approximately three. Across-match algorithm was used to check all pairs of matchedgels for consistency. This algorithm compared the spotsmatched directly between each gel pair to the spots matchedindirectly between the same two gels. If the direct matchdisagreed with the majority of the indirect matches, the directmatch was corrected. Statistical analysis was performedusing the software package XLSTAT 3.5 (Thierry Fahmy). Twocomplete, independent time-course growth experiments wereanalysed.

Acknowledgements

The technical assistance of Günther Boguth and ChristianObermaier is gratefully acknowledged. The DOE JointGenome Institute (JGI) is also acknowledged for the per-mission to use preliminary sequence data from the N.punctiforme ATCC 29133 genome at http://www.jgi.doe.gov/JGI_microbiol/html/nostoc/nostoc_homepage.html.

Supplementary material

The following material is available from http://www.blackwell-science.com/products/journals/suppmat/mole/mole3209/mmi3209sm.htmFig. S1. Micropreparative two-dimensional electrophoresisgels of subcellular protein fractions from Nostoc communeDRH1 cultures grown without UV-B.Table S1. List of protein spots that were significantly affectedby UV-B treatment (1.0 Wm-1).

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Documents

The UV-B stimulon of the terrestrial cyanobacterium Nostoc commune comprises early shock proteins and late acclimation proteins