The LATERAL ORGAN BOUNDARIES gene defines a novel, plant-specific gene family

The LATERAL ORGAN BOUNDARIES Gene Defines a Novel,Plant-Specific Gene Family 1

Bin Shuai,Cristina G.Reynaga-Pen ?a 2,and Patricia S.Springer*

Department of Botany and Plant Sciences,University of California,Riverside,California,92521–0124

The LATERAL ORGAN BOUNDARIES (LOB )gene in Arabidopsis defines a new conserved protein domain.LOB is expressed in a band of cells at the adaxial base of all lateral organs formed from the shoot apical meristem and at the base of lateral roots.LOB encodes a predicted protein that does not have recognizable functional motifs,but that contains a conserved domain (the LOB domain)that is present in 42other Arabidopsis proteins and in proteins from a variety of other plant species.Proteins showing similarity to the LOB domain were not found outside of plant databases,indicating that this unique protein may play a role in plant-specific processes.Genes encoding LOB domain proteins are expressed in a variety of temporal-and tissue-specific patterns,suggesting that they may function in diverse processes.Loss-of-function LOB mutants have no detectable phenotype under standard growth conditions,suggesting that LOB is functionally redundant or required during growth under specific environmental conditions.Ectopic expression of LOB leads to alterations in the size and shape of leaves and floral organs and causes male and female sterility.The expression of LOB at the base of lateral organs suggests a potential role for LOB in lateral organ development.

The shoot apical meristem (SAM)is a group of cells at the growing tip of a plant that is formed during embryogenesis and is maintained throughout its life.The SAM is organized into a central zone composed of slowly dividing stem cells and a peripheral zone containing more rapidly dividing cells that become incorporated into organ primordia.Thus,the SAM serves as the source of cells for all initiating lateral organs of the https://www.wendangku.net/doc/be16654582.html,ans initiate in a specific pattern that depends on the positioning of founder cells in the peripheral zone.This pattern is controlled by a combination of genetic and environmental fac-tors (Steeves and Sussex,1989).Maintenance of the SAM requires a balance between the pool of central stem cells and the flanking peripheral zone cells.A number of genes required for SAM initiation and maintenance have been identified.Proper meristem function requires the competing action of the CLAVATA (CLV)signaling pathway and the tran-scription factor WUSCHEL (WUS)(for review,see Clark,2001).The CLV pathway is required to limit the number and position of stem cells in the meristem by restricting the domain of WUS expression.In con-trast,WUS is required for stem cell maintenance and is thought to act on the CLV pathway by positively regulating expression of the putative ligand encoded by CLV3.The interaction between CLV and WUS is

thought to function as a feedback loop to limit mer-istem size (Brand et al.,2000;Schoof et al.,2000).The class 1KNOX homeobox genes are also impor-tant for SAM function.Class 1KNOX genes are spe-cifically expressed in the SAM and are down-regulated in lateral organ anlage in a number of plant species (Jackson et al.,1994;Long et al.,1996;Nish-imura et al.,1999;Sentoku et al.,1999).Loss-of-function mutations in the Arabidopsis SHOOT MER-ISTEMLESS (STM )or maize (Zea mays )Knotted1genes demonstrate that class 1KNOX genes are im-portant for SAM formation and maintenance (Long et al.,1996;Vollbrecht et al.,2000).One apparent func-tion of STM is to negatively regulate expression of the ASYMMETRIC LEAVES1(AS1)gene in the mer-istem (Byrne et al.,2000).AS1encodes an MYB do-main transcription factor that is a homolog of the Antirrhinum PHANTASTICA and maize ROUGH SHEATH2genes.These genes all show expression in lateral organ primordia (Waites et al.,1998;Timmer-mans et al.,1999;Tsiantis et al.,1999;Byrne et al.,2000).as1mutants are epistatic to stm ,such that as1stm double mutants form a vegetative meristem.These observations suggest that the loss of a meris-tem in stm mutants is due to expression of AS1in the meristem (Byrne et al.,2000).In turn,AS1activity is needed to repress KNOX gene expression in the leaf (Byrne et al.,2000;Ori et al.,2000).

Formation of a proper SAM is closely tied to boundary formation and organ separation,as stm mutants show limited fusion at the cotyledon base (Barton and Poethig,1993).The cup-shaped cotyledon (cuc )mutants also lack a SAM and show extensive cotyledon fusion (Aida et al.,1997).The CUC genes are expressed at the boundary between the SAM and cotyledon primordia,and their activity is required

1This work was supported by the National Science Foundation (grant no.IBN–9875371to P.S.).

*Corresponding author;e-mail patricia.springer@https://www.wendangku.net/doc/be16654582.html,;fax 909–787–4437.2

Present address:Departamento de Ingenier?′a Gene ′tica,CIN-VESTAV Unidad Irapuato,Irapuato,Gto.CP 36500,Mexico.

Article,publication date,and citation information can be found at https://www.wendangku.net/doc/be16654582.html,/cgi/doi/10.1104/pp.010926.

_________________________________________________________________________________________________________This article is published in Plant Physiology Online, Plant Physiology Preview Section, which publishes manuscripts accepted for publication after they have been edited and the authors have corrected proofs, but before the final, complete issue is published online. Early posting of articles reduces normal time to publication by several weeks.

_________________________________________________________________________________________________________

for STM expression(Aida et al.,1999;Takada et al., 2001).We have identified a novel gene that is ex-pressed at the adaxial base of initiating lateral or-gans.The LATERAL ORGAN BOUNDARIES(LOB) gene encodes a plant-specific protein of unknown function.The LOB protein contains a conserved ap-proximately100-amino acid domain that is found in 42other Arabidopsis proteins.Although the function of LOB is unknown,its expression indicates a poten-tial role in organ separation or other aspects of lateral organ development.

RESULTS

?-Glucuronidase(GUS)Expression in the Transposant Line ET22

In a screen for gene-trap expression patterns in the shoot apex of Arabidopsis seedlings(P.Springer and R.Martienssen,unpublished data),an enhancer trap line(ET22)was identified that showed GUS reporter gene activity in defined regions around the SAM.We examined GUS expression in ET22plants throughout development.GUS activity in ET22embryos was first detected at the torpedo stage,and was localized throughout the embryo(Fig.1A).GUS activity be-came progressively localized to the shoot and root apices during later stages of embryogenesis.In ma-ture embryos,GUS activity was confined to the shoot apex and root tip(Fig.1B).Following germination, GUS activity was detected in a band of cells at the base of the cotyledons and leaf primordia(Fig.1,C and D).Longitudinal and transverse sections through the shoot apex revealed that GUS activity was confined to an adaxial domain that was three to five cells deep(Fig.1D and data not shown).GUS expression persisted at the base of expanded

and Figure1.Analysis of GUS activity in ET22enhancer trap line and p LOB5.0::GUS transformants.ET22(A–G).p LOB5.0::GUS

transformants(H–J).A,Torpedo-stage embryo.B,Mature embryo.C,Four-day-old seedling;arrow marks cells at base of

cotyledons,and arrowhead marks cells at base of leaf primordia.D,Transverse section through9-d-old seedling apex

showing GUS staining on the adaxial side of leaf bases.S,SAM;lp,leaf primordium.E,Inflorescence.F,Lateral root.G,

Longitudinal section through lateral root primordium.H,Seven-day-old seedling.I,Inflorescence.J,Lateral root.The tissue

in G was counter-stained with Safranin-O after sectioning.Scale bar?50?m in A and B;?100?m in C,D,F–H,and J;

and?1mm in E and I.

Shuai et al.

mature leaves(data not shown).A similar expression pattern was seen at the base of all lateral organs formed from vegetative,inflorescence,and floral meristems(Fig.1E).GUS activity was also detected in the anthers of the flower(Fig.1E).In the root,GUS activity was detected at the junction between the primary root and lateral root primordia,in a ring of cells at the base of the lateral root(Fig.1,F and G). Expression was maintained at the base of fully de-veloped lateral roots.

Isolation of the LOB Gene

DNA gel-blot hybridization was used to determine that the ET22transposant line possessed a single DsE element(data not shown).Thermal asymmetric in-terlaced(TAIL)-PCR(Liu et al.,1995;Tsugeki et al., 1996)was used to amplify genomic DNA flanking the DsE element.Sequence of the TAIL-PCR product matched that of P1clone MDC12on chromosome5. Genomic DNA fragments from the region around the insertion site were amplified and used as probes to screen a cDNA library derived from floral buds(Wei-gel et al.,1992).Two overlapping cDNA clones were isolated and sequenced.5?-RACE-PCR(Frohman et al.,1988)was used to identify a full-length cDNA sequence(data not shown).Based on the expression pattern of the GUS reporter gene in the transposant line,the corresponding gene was named LOB.The MDC12sequence has recently been annotated,and the LOB gene corresponds to hypothetical gene At5g63090(MDC12.5).At5g63090is identical to LOB throughout the coding region,but does not contain 5?-and3?-untranslated regions(UTRs)that were de-fined by the cDNA https://www.wendangku.net/doc/be16654582.html,parison of the LOB cDNA and genomic DNA sequences showed the presence of one intron in the5?-UTR,with an open reading frame completely contained within the last exon.The DsE insertion was near the3?end of LOB and was inserted such that the GUS gene was tran-scribed opposite to LOB(Fig.2A).

The LOB gene encodes a deduced polypeptide of 186amino acids(Fig.2B)with a predicted molecular mass of20.2kD.Database searches did not identify similarity to known proteins in any species or to any known functional motifs.However,a number of hy-pothetical or unknown proteins in the Arabidopsis genome that were similar to LOB were identified.We have named this region of similarity,which spans approximately100amino acid residues,the LOB do-main(Fig.2B).Expressed sequence tag(EST)se-quences corresponding to related genes from soy-bean(Glycine max),maize,rice(Oryza sativa),tomato (Lycopersicon esculentum),Lotus japonicus,Medicago truncatula,pine(Pinus sylvestris),aspen(Populus spp.),wheat(Triticum aestivum),and potato(Solanum tuberosum)were also identified.Similar genes were not identified in other species,indicating that the LOB domain proteins are unique to plants.

Expression of LOB

To confirm that GUS activity in the ET22trans-posant line accurately reports LOB expression,we constructed two different LOB-promoter::reporter fu-sion constructs.p LOB2.8::GUS contains the5?-UTR and1.1kb of genomic DNA upstream of the putative transcription start site fused to the uidA gene. p LOB5.0::GUS contains the5?-UTR and 3.3kb of genomic DNA upstream of the putative transcription start site fused to the uidA gene.These constructs were introduced into Arabidopsis ecotype Landsberg erecta.GUS expression patterns were examined in seven independent transgenic lines containing p LOB2.8::GUS and in24independent transgenic lines containing p LOB5.0::GUS.GUS activity was nearly ubiquitous in two of the p LOB2.8::GUS lines and in six of the p LOB5.0::GUS lines(data not shown). These insertions were assumed to be adjacent to strong promoter or enhancer sequences that affected activity of the LOB promoter.In the remaining trans-formants for each construct,GUS activity

generally

Figure2.ET22genomic structure and sequence

of LOB.A,Structure of genomic DNA near the

DsE insertion in ET22.Boxes represent exons

and arrows show the direction of transcription.

B,Amino acid sequence of LOB.The LOB do-

main is highlighted in gray,and conserved C

and GAS blocks are underlined with solid and

dashed lines,respectively.The double underline

marks the predicted coiled coil.Invariant Cys

and Pro residues are shown with dots.?,The

site of insertion of the T-DNA in lob-2.?,The

site of insertion of DsE in ET22.

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

mimicked the activity of the ET22transposant line. However,the p LOB2.8::GUS transformants typically showed weaker and more variable GUS expression than the transposant line(data not shown).In addi-tion,the onset of GUS expression in floral buds was later than in the ET22line,and GUS activity was occasionally detected in the leaf blade(data not shown).GUS activity in the remainder of the p LOB5.0::GUS transformants resembled the pattern of the transposant line in the shoot apex(Fig.1H),the inflorescence(Fig.1I),and the root(Fig.1J).How-ever,GUS activity was not detected in the anthers of p LOB5.0::GUS transformants(Fig.1I),suggesting that some regulatory elements were missing from this promoter sequence.

To investigate the possibility that GUS activity in the transposant line was influenced by neighboring genes,expression of the adjacent gene At5g63080 (MDC12.4)was examined.At5g63080is3?to LOB and is transcribed in the same orientation,such that the5?end of At5g63080is6.5kb from the start of transcrip-tion of the GUS gene in ET22(Fig.2A).At5g63080 encodes an unknown protein.An EST sequence cor-responding to At5g63080was identified from a de-veloping seed cDNA library(White et al.,2000).We could not detect expression of At5g63080using re-verse transcriptase(RT)-PCR in any vegetative or floral tissues(data not shown).The neighboring gene on the5?side of LOB,At5g63100(MDC12.6),is5.6kb from the site of insertion,placing it approximately 11.6kb from the start of transcription of the GUS gene(Fig.2A).Expression of At5g63100was not examined.

Attempts to detect LOB transcripts using in situ hybridization were unsuccessful,suggesting that LOB transcripts are present at low abundance.There-fore,we examined the expression pattern of LOB by RT-PCR(Fig.3A).The expression pattern of LOB shown by RT-PCR was consistent with the GUS ex-pression pattern in the trap line.Amplified fragments

were detected in RNA isolated from6-d-old seed-lings,inflorescence stems,roots,buds,and open flowers(Fig.3A).Amplification of a faint band was detected from RNA isolated from rosette and cauline leaves(which included the leaf base).LOB expression was not detected in an RNA sample isolated from the apical one-half of rosette leaves(data not shown). Based on the sequence of the largest cDNA clone characterized,the LOB-specific primers were ex-pected to amplify a245-bp PCR product.Several amplified products were detected(Fig.3A),includ-ing one of the expected size.Sequencing of the RT-PCR products demonstrated that the multiple PCR products were derived from alternatively spliced LOB transcripts.Four different splice variants were identified in the5?-UTR(Fig.3B).The LOBa and LOBb transcripts differed by four nucleotides at the splice donor site.LOBa,which was identical to the original cDNA sequences,used a non-consensus GC at the splice donor site.The LOBb transcript used a consensus GU splice donor site four nucleotides downstream of the LOBa site(Fig.3B).Use of a5?-GC is unusual;however,1%of Arabidopsis introns have a GC in the5?position(Brown et al.,1996).The remainder of the nucleotides at the splice site con-form to the consensus sequence.The RT-PCR prod-ucts derived from the LOBa and LOBb transcripts could not be resolved on agarose gels,but cloning and sequencing of16clones suggested that the two transcripts were present at similar levels in seedlings. The LOBc and LOBd transcripts used the LOBa splice donor site and included an additional exon that dif-fered at its3?end(Fig.3B).These larger transcripts appeared to be present at lower levels than LOBa and LOBb,based on band intensities of the RT-PCR products.

All four5?-UTR splice variants are predicted to encode an identical protein,as the predicted

open Figure3.Expression of LOB in wild-type tissues.A,RT-PCR analysis of LOB expression.RNA was isolated from Landsberg erecta6-d-old seedlings(S),rosette leaves(RL),cauline leaves(CL),stem(ST),root (RT),flower buds(B),and open flowers(FL).The four products are indicated by arrows.The lower panel shows RT-PCR using primers to the ACT2gene as a control.B,Schematic showing the four LOB transcripts that are produced due to alternative splicing in the5?-UTR.Boxes represent exons,and lines represent introns.The pair of arrows indicates the location of the primers used in the PCR reac-tions.Exon positions in the individual transcripts are 1..296, 1673..2402(LOBa);1..300,1673..2402(LOBb);1..296,1046..1104, 1673..2402(LOBc);1..296,1046..1175,1673..2402(LOBd).Posi-tion1indicates the putative start of transcription and corresponds to position19,609of MDC12(AB008265);position2,402corresponds to position17,208.Accession numbers for each transcript are AF447897(LOBa),AF447898(LOBb),AF447899(LOBc),and AF447900(LOBd).

Shuai et al.

reading frame is not affected.However,the addi-tional exon introduces out of frame AUG codons upstream of the translation start site in both of the larger transcripts.If these upstream AUGs were used,they could perhaps affect translation initiation of the downstream open reading frame.It is not clear if translation would initiate at any of the out of frame AUGs,however,as none of them occurs in a consen-sus context(Joshi et al.,1997).

Alterations in Expression of LOB

The transposant line ET22contains a DsE insertion in the3?end of the LOB gene,corresponding to the non-conserved C terminus of the LOB protein(Fig.2, A and B).To determine whether the insertion af-fected LOB transcript accumulation,RT-PCR was used to examine LOB expression in seedlings that were homozygous for the DsE insertion.After30 PCR cycles,a LOB-specific PCR product could be readily amplified from cDNA derived from6-d-old wild-type seedlings(Fig.3A).In contrast,only a faint band could occasionally be detected after amplifica-tion of cDNA derived from lob::DsE homozygotes, suggesting that the DsE insertion causes a reduction in LOB transcript levels(data not shown).Reconstruc-tion experiments using20cycles of PCR,followed by blotting and hybridization,demonstrated that LOB transcript abundance is reduced20-to50-fold com-pared with wild type in lob::DsE homozygotes(data not shown).Despite the significantly reduced LOB transcript levels,no obvious morphological pheno-types were visible in lob::DsE homozygotes.

To identify additional loss-of-function lob muta-tions,we screened the Arabidopsis Knock-Out Facil-ity’s T-DNA insertion collection(Krysan et al.,1999) and identified a T-DNA insertion in the conserved LOB domain(Fig.2B).This allele was designated lob-2.RT-PCR showed that full-length LOB tran-scripts did not accumulate in plants homozygous for the T-DNA insertion(data not shown).Examination of lob-2homozygotes again revealed no obvious vis-ible phenotypes in plants grown under standard growth conditions.

To determine the effect of expression of LOB out-side of its normal expression domain,the LOB coding sequence was fused to the cauliflower mosaic virus 35S promoter and introduced into wild-type Arabi-dopsis plants.Thirty-seven independent transfor-mants were recovered,and25of them showed a similar phenotype(Fig.4),whereas the remaining nine transformants resembled wild-type plants. Fewer transformants were recovered than in control experiments using empty vector or other transgenes (data not shown),suggesting that high levels of LOB expression may be detrimental.RNA-blot analysis was performed on individual transformants to verify LOB overexpression(Fig.4M).Plants overexpressing LOB were much smaller than wild type at all stages of development(Fig.4,B and C).35S::LOB rosette leaves had short petioles and were more rounded than wild type(Fig.4,B–E).Leaves were often curled upward(Fig.4,D and E).After flowering,the inflo-rescence stem did not elongate appreciably,resulting in a tightly packed cluster of flowers(Fig.4D). 35S::LOB plants produced abnormal flowers that con-tained reduced floral organs and were infertile.Or-gans in the outer three whorls failed to elongate, resulting in exposed gynoecia(Fig.4,G and H). Anthers only rarely produced pollen grains.Al-though35S::LOB carpels elongated and the stigma occasionally appeared to develop normally,pollina-tion with wild-type pollen did not result in the pro-duction of seeds,suggesting that35S::LOB plants are female sterile.We examined35S::LOB leaves by clearing and viewing with DIC optics.Cell size and shape were similar to that of wild type(Fig.4,I–L).In addition,35S::LOB leaves appeared to have a normal arrangement of cells in transverse section(data not shown).

The LOB Domain Gene Family

The Arabidopsis genome database was searched to identify all Arabidopsis genes related to LOB. Searches were performed using TBLASTN with the entire LOB amino acid sequence as a query.A total of 42genes was identified in the Arabidopsis genome that showed similarity to LOB(Table I).All42pre-dicted proteins share varying degrees of similarity in the LOB domain(Fig.5,A and B).No genes were identified that were similar to the carboxy-terminal 75residues of LOB,suggesting that this region of the LOB protein is unique.

EST sequences were available for13of the LBD genes(Table I).cDNA clones corresponding to ESTs for LBD6,13,15,18,25,29,30,37,41,and42were obtained from the Arabidopsis Biological Resource Center(Ohio State University,Columbus),Kazusa DNA Research Institute(Chiba,Japan),or Genome Systems Inc.(St.Louis)and were fully sequenced. We also isolated and sequenced a cDNA clone cor-responding to LBD16.In most cases,the cDNA se-quences agreed with the annotated gene models and included5?-and3?-UTRs.In the case of LBD13,an additional intron was present relative to the anno-tated gene model,resulting in a change in the first four residues in the amino terminus of the deduced protein.The LBD18cDNA sequence differed from the predicted gene model at a splice acceptor site. This change resulted in an insertion of five amino acids in the deduced protein sequence,which al-lowed a better alignment with the other LBD protein sequences(Fig.5A).Although a cDNA clone was not available for LBD31,examination of the gene model revealed a similar situation to LBD18,and movement of the position of a splice acceptor site also resulted in an insertion of five amino acids,allowing better

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

alignment to the consensus.The LBD25cDNA se-quence extended the 5?end of the first exon relative to the gene model.This extended the open reading frame,adding 31amino acids to the amino terminus of the deduced protein sequence.The cDNA se-quences have been deposited in GenBank and acces-sion numbers are shown in Table I.

Genes encoding LBD proteins fall into two classes.Members of class I include 36Arabidopsis genes that are predicted to encode proteins that are similar to LOB (25%–82%identity)throughout the LOB domain

(Fig.5A).Class II consists of six Arabidopsis genes that encode deduced proteins that are less similar to LOB (28%–33%identity)and the other class I pro-teins (Fig.5B).Class II proteins share a conserved amino terminus (62%–93%identity in pair-wise com-parisons).The class II proteins share limited se-quence conservation outside of the LOB domain as well.Signature sequences that define class I and class II proteins were identified (see below).

To identify potential functionally important do-mains within the class I and class II proteins,

blocks

Figure 4.Phenotypes of transgenic plants that ectopically express LOB .A,Wild-type 19-d-old Landsberg erecta plant.B and C,Two independent transgenic 35S ::LOB plants (19-d-old).D,Thirty-two-day-old 35S ::LOB plant.E,Scanning electron microscopy of 35S ::LOB rosette leaf.F,Wild-type Landsberg erecta flower.G,35S ::LOB flower.H,Scanning electron microscopy of 35S::LOB flower.I through L,Differential interference contrast (DIC)images of wild-type (I and K)and 35S::LOB (J and L)cleared rosette leaves.The images show the epidermis (I and J)and mesophyll (K and L).M,Northern-blot analysis of LOB expression in wild-type and five different 35S ::LOB transgenic plants.Ten micrograms of total RNA was loaded in each lane.The filter was probed with the LOB cDNA (top)or 18S rDNA as a loading control (bottom).Scale bar in A through C ?5mm;in I through L ?50?m.

Shuai et al.

Table I.Arabidopsis genes encoding LOB domain proteins

Gene Bacterial Artificial

Chromosome/P1

Locus

Genbank

Protein ID

Chromosome

Locus a

Accession No.Clone Representing EST Sequence b,c

Class I

LOB MDC12.510177290At5g63090BAB10551

LBD1F24B9.18439879At1g07900AAF75065

LBD2F9P14.148844133At1g06280AAF80225

LBD3F3O9.334966373At1g16530AAD34704

LBD4T19E23.116692123At1g31320AAF24588

LBD5T22A15.812324709At1g36000AAG52312

LBD6F5I14.152190548At1g65620AAB60912VBVYB03

LBD7F3N23.185903087At1g72980AAD55645

LBD8F3P11.114191781At2g19510AAD10150

LBD9F6F22.153687236At2g19820AAC62134

LBD10F27L4.153152616At2g23660AAC17095

LBD11T17D12.64510398At2g28500AAD21485

LBD12T27E13.133150407At2g30130AAC16959

LBD13T9D9.152347197At2g30340AAC16936RZ93g04,RZ123h01

LBD14F16D14.154432826At2g31310AAD20676

LBD15T2P4.182651309At2g40470AAB87589241G2,701514676,600038330

LBD16MHK10.154567314At2g42430AAD23725

LBD17MHK10.164567315At2g42440AAD23726

LBD18F4L23.72583113At2g45420AAB82622M13A6,M22C7

LBD19F4L23.82583114At2g45410AAB82623

LBD20F20H23.216006865At3g03760AAF00641

LBD21F9F8.106016686At3g11090AAF01513

LBD22MCP4.89294609At3g13850BAB02910

LBD23MLJ15.2At3g26620

LBD24MLJ15.6At3g26660

LBD25MGF10.69294470At3g27650BAB02689701546372

LBD26K24A2.39294310At3g27940BAB01481

LBD27T23J7.2004741204At3g47870CAB41870

LBD28T20E23.1106561991At3g50510CAB62480

LBD29F9D24.1006735331At3g58190CAB68157RZ58d08

LBD30F6N15.43193318At4g00220AAC19300232A14,701500638,SQ185e01

LBD31F6N15.253193312At4g00210AAC19294

LBD32T12H17.902827547At4g22700CAA16555

LBD33K16F4.48978344At5g06080BAA98197

LBD34F2G14Not annotated d

LBD35MIK22.2110176709At5g35900BAB09931

LBD36MUD21.139758137At5g66870BAB08629

Class II

LBD37K8K14.169758441At5g67420BAB09027AA07F04,AB01G02,APD23d08,APD43f11,

APZ06a08,OBO52,RZ108b01,RZ126f11,47B5,

65DI,179D12,217P3,240N2,701551301 LBD38F3A4.206522915At3g49940CAB62102147D14T7,VBVQC02

LBD39F19F18.304468979At4g37540CAB38293701500839,165E11T7,RZ23c09

LBD40F5A8.24204277At1g67100AAD10658M11G10,M13C9,M15B4,M22A4,M53F11 LBD41F16B3.186957718At3g02550AAF32462RZ101f04,SQ182b06,SQ193f07,111E10,195F24,

701667942

LBD42T26J14.812324879At1g68510AAG52389SQ124h04

a Designation from Munich Information Center for Protein Sequences Arabidopsis thaliana Database(MATDB)(www.mips.biochem.mpg.de/proj/thal/db/index. html).

b Clones shown in bold were fully sequenced.

c EST accession nos.:Z33806,Z25656,AF447887(clone VBVYB03);AV554524(clone RZ93g04); AV551296,AV538901,AF447888(clone RZ123h01);N97300(clone241G2);AI993799,AF447889(clone701514676);BE529105(clone600038330);BE520513, BE520514,AF447891(clone M13A6);BE521897,BE521898(clone M22C7);AI998629,AF447892(clone701546372);AV553261,AV544763,AF447893(clone RZ58d08);AI994962(clone701500638);AV563330(clone SQ185e01);N65781,AF432232(clone232A14);BE038006(clone AA07F04);BE038601(clone AB01G02);AV525400(clone APD23d08);AV518911(clone APD43f11);AV526154,AV520071(clone APZ06a08);F14269,F14441(clone OBO52);AV550089 (clone RZ108b01);AV539081,AV551431,AF447894(clone RZ126f11);T14105(clone47B5);T41721(clone65D1);H36818(clone179D12);N38449(clone 217P3);N65652(clone240N2);AI996949(clone701551301);T76164(clone147D14);Z29130,F13856(clone VBVQC02);AI994989(clone701500839);R65200 (clone165E11);AV552189(clone RZ23c09);BE520344(clone M11G10);BE520541(clone M13C9);BE520808,BE520809,BE520810(clone M15B4);BE521846, BE521847(clone M22A4);AV537704,AV549715,AF447895(clone RZ101f04);AV563144(clone SQ182b0);AV563797(clone SQ193f07);AI100279,T42227 (clone111E10);H76116(195F24);AI996685(clone701667942);AV559860,AF447896(clone SQ124h04);AF447890(LBD16).Accession nos.shown in italics represent the complete sequence of the corresponding clone.

d Complement(AL391146.1:60133.60555).

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

were generated with Block Maker (Henikoff et al.,1995).These analyses defined two conserved blocks in the class I proteins (Fig.5A).The C block is 22amino acids in length and contains four absolutely conserved Cys residues in a CX 2CX 6CX 3C motif.

LBD3deviates from this motif slightly,containing four amino acids between the third and fourth Cys residues (Fig.5A).The GAS block is 49amino acids in length,beginning with a FX 2VH motif and ending with a DP(V/I)YG motif (Fig.5A).The Pro residue

in

Figure 5.(Continues on facing page .)

Shuai et al.

the DP(V/I)YG signature is present in all class I proteins.

Three conserved blocks were detected in the class II proteins that together span the entire length of the LOB domain.These blocks are in close proximity to each other and therefore will be considered as one large block (Fig.5B).The class II block contains a Cys motif similar to the class I proteins.Spacing between the four Cys residues is the same in both classes,but the intervening amino acids differ.The class I con-sensus sequence is C AA C KFLRRK C X 3C ,whereas the class II consensus sequence is C NG C RVLRKG C-SE(D/N)C .The class II block contains an invariant Pro residue that is also found in the DP(V/I)YG signature in the class I LOB domains.One distin-guishing feature of the class II proteins is that they are more Cys rich than the class I proteins,containing from nine to 13total Cys residues,whereas the class I proteins contain four to seven cysteines.

Examination of the LOB protein sequence for pos-sible secondary structure revealed a predicted coiled coil of 30amino acids in length at the end of the LOB domain.The predicted coiled coil contains four

leucines in a LX 6LX 3LX 6L spacing that is reminiscent of a Leu-zipper (Landschultz et al.,1988).To deter-mine whether this potential structural domain is con-served,the LBD protein sequences were examined for predicted coiled-coil structures.Among the class I proteins,33of the 36proteins were predicted to form a coiled coil at the end of the LOB domain with ?90%probability.LBD2,26,and 34were not pre-dicted to form coiled-coils.None of the class II pro-teins were predicted to form coiled-coil structures.

Expression of LBD Genes

Twenty-nine of the 42LBD genes were hypothetical in that they were predicted from genomic sequence but had not experimentally been shown to be ex-pressed.We performed RT-PCR to examine the pat-terns of expression of 30different LBD genes in a variety of Arabidopsis tissues.In all cases,primers spanning predicted introns were used to distinguish between amplification of genomic DNA and ampli-fication of cDNA.Expression was detected for 24LBD genes (Fig.6).No expression was detected

for

Figure 5.(Continued from facing page .)

A,Alignment of the LOB domains of class I protein sequences.LBD34is not included in the alignment because the annotation is not certain.B,Alignment of LOB with the class II protein sequences.The alignments were produced by the Alignment program of Vector NTI,which uses the Clustal W algorithm.Conserved amino acids are highlighted in black,and similar amino acids are highlighted in gray.The conserved blocks and invariant residues are shown above the alignments.

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

LBD5,8,9,23,24,and 42in any of the tissues tested.Only one of these genes,LBD42,is represented by an EST sequence.At this time,we do not know if LBD5,8,9,23,and 24are expressed at levels that were undetectable under the conditions used,or are ex-pressed in tissues that were not tested.It is also possible that these genes are pseudogenes.

LBD gene expression patterns were quite variable,with many genes showing tissue or developmental stage-specific patterns (Fig.6).Transcripts from LBD1,3,4,6,15,25,37,38,39,and 41were detected in all tissues examined,although at variable levels.LBD11transcripts were detected in all tissues except root.LBD17transcripts were detected in all tissues except 12-d-old shoots.Transcripts from LBD14,29,

and 33were detected only in roots,whereas tran-scripts from LBD16were primarily detected in roots,but a faint band was also amplified in shoots.In vegetative tissues,LBD12was also expressed pre-dominantly in roots;low levels were detected in shoots and floral stems.LBD12transcripts were also detected in open flowers,but not flower buds.LBD19transcripts were detected in shoots,roots,and floral tissues,but not in stems or leaves.LBD13transcripts were detected in shoots and roots but not in rosette or cauline leaves or inflorescence stems.Low levels were also detected in floral buds and open flowers.Transcripts from LBD20and 40were detected in roots and floral tissues,although at different levels.Transcripts from LBD18and 30were not detected in shoots or rosette leaves,but were present in all other tissues tested.LBD31transcripts were detected in roots,stems,and floral tissues.

DISCUSSION

The LOB gene was identified based on the expres-sion pattern of an enhancer trap insertion.Although we were not able to visualize LOB transcript local-ization,a LOB promoter::GUS fusion largely recapit-ulated the expression pattern of GUS in the ET22line.The p LOB 5.0::GUS fusion differed from the trans-posant line in that it did not drive expression in anthers.This raises the possibility that sequences within the LOB coding region or 3?to the gene con-tribute to its expression.Another possible explana-tion is that the anther staining in ET22plants does not reflect expression of LOB .The DsE insertion in LOB is oriented so that the GUS gene is transcribed opposite to LOB .This could place GUS under the control of 3?regulatory elements or cryptic enhancers that do not normally function.Differences between the expression patterns conferred by the two p LOB ::GUS constructs indicate the presence of en-hancer elements in the region of the promoter unique to p LOB 5.0::GUS .

LOB is expressed at the base of lateral organs in the shoot and the root (Fig.1).No obvious morphologi-cal characteristics distinguish LOB -expressing cells from adjacent cells that do not express LOB .One possible function of genes expressed in such a pat-tern is to define a boundary between the initiating organ primordia and the stem cells they are derived from.As lateral organs initiate in the shoot and the root,founder cells from the SAM and pericycle,re-spectively,are recruited into forming lateral organs (Steeves and Sussex,1989;Laskowski et al.,1995).The establishment of a boundary between a primor-dium and its progenitor cells is likely important for maintaining the integrity of the stem cells and the initiating organ primordium.

A number of plant genes that are expressed in the vegetative shoot apex in a pattern similar to LO

B have been described,including UNUSUAL

FLORAL

Figure 6.RT-PCR analysis of the expression profiles of 24different LBD genes.SH,Twelve-day-old shoot tissue;RL,rosette leaves;CL,cauline leaves;ST,inflorescence stem;RT,root;BD,floral buds;FL,open flowers.

Shuai et al.

ORGANS(UFO),NO APICAL MERISTEM,CYP78A5, and the CUP-SHAPED COTYLEDON1(CUC1)and CUC2genes(Souer et al.,1996;Aida et al.,1997;Lee et al.,1997;Zondlo and Irish,1999;Takada et al., 2001).Analyses of loss-of-function mutations sup-port the idea that some of these genes are important for the establishment of a boundary between organs. Mutations in no apical meristem cause a loss of the SAM and fusion of the cotyledons.CUC1and CUC2 are functionally redundant and cuc1cuc2double mu-tants have fused cotyledons and do not form a SAM. ufo mutants have aberrant floral organs,but no veg-etative phenotypes,suggesting that UFO acts redun-dantly in the vegetative shoot apex.Based on GUS activity in the transposant line,LOB expression ap-pears to commence later in leaf initiation than that of UFO or CUC2.Although it is possible that LOB is expressed earlier,but at levels that are not detectable using the GUS reporter,these observations may in-dicate that LOB functions in the later stages of leaf development.Other possible functions for a gene expressed in such a domain are involvement in con-trol of cell division or differentiation at the leaf base, establishment of adaxial cell fates,or functions in abscission.The Arabidopsis HAESA Leu-rich repeat receptor kinase,which is required for proper abscis-sion of floral organs,is expressed in a pattern similar to LOB(Jinn et al.,2000).HAE expression appears to initiate later than that of LOB however.

Two different lob mutations were identified,and we examined homozygous mutant plants for abnor-mal morphology.Plants that contained a disrupted LOB gene made reduced levels of LOB transcript in the case of lob::DSE or a truncated transcript in the case of lob-2.In both cases,homozygotes were viable and had normal morphology under standard growth conditions.These data may indicate that LOB is func-tionally redundant,or required under a particular growth condition that we did not examine.Further support for functional redundancy comes from the fact that the LOB gene lies within a duplicated region of the Arabidopsis genome(The Arabidopsis Ge-nome Initiative,2000).The corresponding region lies on chromosome3and contains the LBD27gene. However,LBD27is only41%identical to LOB in the LOB domain.Another LOB domain protein,LBD25, also encoded by a gene on chromosome3,is83% identical to LOB in the LOB domain.Phylogenetic analyses also place LOB and LBD25in the same clade and LBD27in a different clade(B.Shuai and P. Springer,unpublished data).For this reason,LBD25 may be more likely to have functions that overlap with LOB.Analyses of LBD25transcript distribution by RT-PCR revealed that the LBD25and LOB expres-sion domains overlap,although LBD25expression appears to be broader than LOB(Figs.3A and6). Functionally redundant genes with expression pat-terns that are not identical have been described;for example,the CUC1expression domain is broader than that of CUC2(Takada et al.,2001).Mutations in LBD25will need to be identified to determine if LOB and LBD25are functionally redundant.

Ectopic expression of LOB outside of its normal domain caused pleiotropic defects,making it difficult to attribute a specific role in plant development to LOB.35S::LOB plants made generally smaller organs. The effects on organ size appeared to be largely due to differences in cell numbers,as we could not detect significant differences in cell size(Fig.4,I–L).This may suggest that LOB functions to limit cell division at the base of lateral organs.An alternate possibility is that the effect on cell division is a pleiotropic stress response.

The deduced LOB protein is not similar to any previously described proteins in plants or animals, and does not contain defined functional domains. However,the amino terminal one-half of the LOB protein contains a conserved domain that is present in a large group of plant proteins that have been identified by EST and genomic sequencing.A search of the Arabidopsis genome sequence revealed42 other genes that are predicted to encode LOB domain proteins(Table I).The LBD genes fall into two dis-tinct classes based on sequence similarity to LOB in the LOB domain(Fig.5).Examination of LBD expres-sion profiles revealed that LBD genes are expressed in a variety of different patterns,with some genes being expressed in all tissues tested,whereas other genes were expressed in a more limited fashion(Fig.

6).These data may indicate diverse roles for the LBD genes.

The LOB domain contains conserved blocks of amino acids that identify the LOB domain gene fam-ily.In particular,a conserved CX2CX6CX3C motif, which is the defining feature of the LOB domain,is present in all LBD proteins.It is possible that this motif forms a zinc finger,although the spacing be-tween the cysteines is not typical of a C2/C2type zinc finger(Takatsuji,1998).LOB and many of the class I LOB domain proteins are predicted to form a coiled-coil motif that may function in protein-protein inter-actions.The lack of a predicted coiled coil in the class II proteins suggests that their function may be dis-tinct from the class I LOB domain proteins.

LOB is expressed at low levels,is not present in EST databases,and is apparently functionally redundant, suggesting that LOB is unlikely to have been identi-fied by conventional forward mutagenesis or differ-ential expression approaches.The use of a gene trap approach allowed the identification of LOB,a gene encoding a novel,plant-specific protein of unknown function.The fact that LOB is plant specific could suggest its involvement in processes that are unique to plants.Further characterization of LOB and related LBD genes will be needed for the role of LOB in plant development to be understood.

A major goal in plant biology in the coming years will be to determine the function of every plant gene.

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

Analyses of the annotated regions of the Arabidopsis genome suggest that approximately30%of the25,498 Arabidopsis genes are predicted to encode proteins that cannot be classified into functional groups based on sequence(The Arabidopsis Genome Initiative, 2000).Determining the function of genes in this cat-egory will be especially challenging.The analysis of members of multigene families can be particularly difficult,as these genes may be functionally redun-dant.In these instances,information about a gene’s expression pattern can often provide important in-formation regarding a potential biological role.

MATERIALS AND METHODS

Plant Growth Conditions

Seedlings were grown on germination media as previ-ously described(Springer et al.,2000).Soil-grown plants were grown in Sunshine Mix No.1(SunGro,Bellevue,WA) supplemented with fertilizer and insecticide as previously described(Springer et al.,2000).Plants were grown in a 16-h light:8-h dark cycle(180microeinsteins m?2s?1).

Histochemical Localization of GUS

Activity and Microscopy

Plant tissues were stained for GUS activity in5-bromo-4-chloro-3-indolyl-?-glucuronic acid and were cleared in 70%(v/v)ethanol as previously described(Sundaresan et al.,1995).Stained tissue was processed for sectioning as previously described(Springer et al.,2000)and was viewed with a stereomicroscope or mounted on slides and viewed with DIC optics.Leaves were cleared as described(Berleth and Ju¨rgens,1993)and were viewed with DIC.

Cloning of LOB

Genomic DNA was isolated from pooled F3seedlings as previously described(Springer et al.,1995).TAIL-PCR(Liu et al.,1995)was performed as described(Tsugeki et al., 1996).TAIL-PCR products were cloned using the pGEM-T Easy vector system(Promega,Madison,WI)and were sequenced at the University of Maine DNA sequencing facility(Orono,ME).For cDNA library screening,PCR primers were designed to amplify genomic DNA fragments in the vicinity of the DsE insertion in ET22.Primers MDC5, 5?-GGCATTCAAGCAGGTTTACG-3?;MDC6,5?-AGCTA-ATGCTGACTTGGCAC-3?;MDC7,5?-AAGATTTTGTG-GACGTTGGC-3?;and MDC8,5?-TTGGAAGCGAAATT-CAAAGG-3?were used.MDC5and MDC6amplified a 1.5-kb fragment,and MDC7and MDC8amplified a1.6-kb fragment.Both fragments were labeled using a random-primed DNA labeling kit(Roche Molecular Biochemicals, Indianapolis)and were used together to screen a cDNA library made from Arabidopsis flower buds(Weigel et al., 1992).The library,CD4–6,was obtained from the Arabidop-sis Biological Resource Center.Approximately300,000 clones were screened,and two clones were identified that hybridized to both fragments.To clone the5?end of the LOB cDNA,5?-RACE-PCR was performed as previously de-scribed(Frohman et al.,1988)with the following modifica-tions.First strand cDNA synthesis was performed with the primer5?-RACE O,cDNAs were tailed with terminal trans-ferase,and first round amplification was done with primers Q O,Q T,and5?-RACE O.First round PCR products were reamplified using Q I and nested gene-specific primer5?-RACE I.Conditions for the second round PCR amplification were as follows:45s at94°C,1min at55°C,and1min at 72°C for three cycles;45s at94°C,1min at60°C,and1min at72°C for10cycles;and45s at94°C,1min at55°C,and1 min at72°C for10cycles.The LOB gene-specific primers were5?-RACE O,5?-TTTCTTCCTCTTTCAAGGGC-3?and5?-RACE I,5?-AGGGATCCTTACCCTTTGAATTTCGC-3?.Q T, Q O,and Q I primer sequences have previously been de-scribed(Frohman et al.,1988).

Constructs and Generation of Transgenic Plants

The LOB promoter fragments were amplified from gen-omic DNA using primers pET22–3?:5?-CATGCCATGG ACGACGCCATTTGTTTTTCTT-3?and pET22–5?a:5?-CCG-CTCGAGTTCCCACCACTAACCACCAT-3?(p LOB2.8)or pET22–5?b:5?-TCCCCCGGGTTGCTTGGTCATCGTGTC-TT-3?(p LOB5.0).The primers contained introduced restric-tion sites to facilitate cloning.The amplified p LOB2.8frag-ment was cloned into SLJ4D4,which contains a uidA gene fused to the octopine synthase transcription terminator (Jones et al.,1992).The resulting promoter::GUS fusion was cloned into the binary vector pPZP111(Hajdukiewicz et al., 1994)to create the p LOB2.8::GUS plasmid.The amplified p LOB5.0fragment was fused to the uidA gene and was cloned into the binary vector pCAMBIA3200(Center for the Application of Molecular Biology to International Ag-riculture,personal communication)using the Sma I and Pst I sites to create the p LOB5.0::GUS plasmid.A construct for ectopic expression of LOB was made by introducing the LOB coding region into pPS119(P.Springer and R.Mar-tienssen,unpublished data),which contains the35S cauli-flower mosaic virus promoter(Odell et al.,1985)and a3?octopine synthase transcription terminator(DeGreve et al., 1983)interrupted by multiple cloning sites in a pPZP111 backbone(Hajdukiewicz et al.,1994).The single exon con-taining the LOB coding region was amplified from genomic DNA using PFU polymerase(Stratagene,La Jolla,CA)and primers SET22–5,5?-CCGCTCGAGATGGCGTCGTCATC-AAACTC-3?and SET22–3,5?-GCTCTAGACTCACATGTT-ACCTCCTTGC-3?.Both primers contain introduced restriction sites for cloning.The PCR product was cloned into pBS SK?(Stratagene),sequenced to verify its integrity, and subsequently subcloned into pPS119to create the 35S::LOB construct.Binary vectors were introduced into wild-type Landsberg erecta Arabidopsis plants by floral dip (Clough and Bent,1998).

Scanning Electron Microscopy

Thirty-two-day-old35S::LOB transgenic plants were fixed in3%(v/v)glutaraldehyde(EM Sciences,Fort Wash-

Shuai et al.

ington,PA)in1?phosphate-buffered saline at4°C over-night.Plants were rinsed with1?phosphate-buffered sa-line and dehydrated through an ethanol series at4°C. Dehydrated tissue was critical point-dried in liquid carbon dioxide.Individual leaves were mounted on scanning elec-tron microscope stubs,coated,and observed in a scanning electron microscope(XL30-FEG;Philips,Eindhoven,The Netherlands)at an accelerating voltage of20kV. Screening for T-DNA Insertions in LOB

Primers were designed based on the recommendations of the Arabidopsis Knockout Facility(http://www. https://www.wendangku.net/doc/be16654582.html,/Arabidopsis/).Primers used in the screening were:ET22–4,5?-CACTTTGTCTTTTGCTCTTT-CTCCTTCCT-3?and ET22–5,5?-AAGCAGAGACCTT-CAATTATTAGCACCCT-3?in pair-wise combination with T-DNA left border primer JL-202.After identification of a pool containing a T-DNA insertion in the LOB coding region,seeds from subpools were obtained from the Ara-bidopsis Biological Resource Center.PCR reactions on sin-gle plants were used to identify plants homozygous for the T-DNA insertion.

Expression Analyses

RNA was isolated from various tissues from wild-type plants,and RNA gel-blot hybridizations were performed as previously described(Martienssen et al.,1989).For RT-PCR analysis,cDNA was synthesized from2?g of total RNA using an oligo-(dT)primer and M-MLV RNase H minus reverse transcriptase(Promega).One-twentieth vol-ume of each cDNA sample was used as the template for PCR amplification.Primers MDC7and MDC8(Fig.3B,see above),which flanked an intron in the5?-UTR,were used for amplification of LOB under the following conditions: denaturation at94°C for3min,followed by30cycles of45s at94°C,45s at57°C,and1min at72°C.Control reactions using primers to the ACT2gene(An et al.,1996;Li et al., 2001)were performed on the same cDNA samples.The gene-specific primers used were:LBD1,5?-GGAATCCC-AAATCATTGCTC-3?and5?-TTAGTCCATGTGCTGCT-TGC-3?;LBD3,5?-ACAAAAGGGTCACAGACACG-3?and 5?-AAGACCAAAGGAAGTCTCCG-3?;LBD4,5?-CGTTTT-CTCGCCGTATTTTC-3?and5?-ACTCTCCCAAACTGG-CTTCA-3?;LBD5,5?-CCTGGAGTTCACGGAGGTAG-3?and5?-CCTCTAGGAAACCGTCGTCC-3?;LBD6,5?-ATTT-CCCCTCTGAGCAACAG-3?and5?-AAGACGGATCAA-CAGTACGG-3?;LBD8,5?-TCGTCCTTGCTGCGTATG-TA-3?and5?-TCCACATGATCTTTTGCACC-3?;LBD9,5?-TGCGTAATTCAATTTGCCAC-3?and5?-TCAATGTTAA-ACGTGCTCCTTG-3?;LBD11,5?-TTTGGCACCGTACTTT-CCTC-3?and5?-ATGTCCAAAGAGGATCCCAC-3?;LB-D12,5?-GATCCTCACAAATTCGCCAT-3?and5?-TAA-GAGGGTCTTGCATTTGC-3?;LBD13,5?-TGGGAATCA-GGAGACATGTG-3?and5?-GTGGCGTAGGATTTCCG-TAC-3?;LBD14,5?-TTTTGCAGCCATTCACAAAG-3?and 5?-CAGACCAAGGAAAATTGACC-3?;LBD15,5?-GAAT-GTCCCTTTTCGCCATA-3?and5?-TCTCACTTTCAATGT-TGCCG-3?;LBD16,5?-TCGCAGCTATTCACAAGGTG-3?and5?-CCTCCGGTTTGATGATGAGT-3?;LBD17,5?-AAA-AGGATGTGTGTTTGCCC-3?and5?-ATCAGATTATTGC-CGCCATG-3?;LBD18,5?-AGGTCCGATGCTGTCGTA-AC-3?and5?-ACATAGTTCGAGACGGCGAG-3?;LBD19, 5?-TGAGATTGCCTCTGCACAAG-3?and5?-AAGTGCA-AGCCGGAAGTTTG-3?;LBD20,5?-CATGGTGAAGCTGT-TCATGG-3?and5?-TTTTGGGTCAGACCAAGGAG-3?; LBD23,5?-GAATCCAAAAAGATGTGCAGC–3?and5?-TGGCCTCTTGATTATGAGTCTG-3?;LBD24,5?-GCTAA-TGGCCTCTTGATTATGATT-3?and5?-GAATCCAAAAA-GATGTGCAGC-3?;LBD25,5?-AAGGACCTTTTCTTGT-TGCG-3?and5?-CGCCGCTAATTTTCTCAAAG-3?;LBD29, 5?-TGAGGAGGTTTCGTTGTGGT-3?and5?-CGCTGTGA-AGCCGCTATTA-3?;LBD30,5?-TGCGTCTCTCACATCGT-CTC-3?and5?-ACTGACGAGGCAGAACCACT-3?;LBD31, 5?-CTTACGAGGCATTGGCTAGG-3?and5?-GAAGATG-GTCGGTATTTGCC-3?;LBD33,5?-GGTCGTGGCCATA-GTCATCT-3?and5?-CTAAGGAGGAAATGCAACCG-3?; LBD37,5?-AGATGGTTGGTCTTCCGATG-3?and5?-CCGT-CTTCGTCGCTAAATTC-3?;LBD38,5?-CGTGCCGGTTTA-ATGTCTTT-3?and5?-ACGAAGGTTGTTGTTCCGAC-3?; LBD39,5?-GTGGATCTGGAGGTGGAGAA-3?and5?-CCTC-CGTACCTGAACTCCAA-3?;LBD40,5?-TACGAAAAGGC-TGCAGTGAA-3?and5?-GGTACCACCACGTGATTTCC-3?; LBD41,5?-TCCTTCATGAGCAGCCACTA–3?and5?-AAACCAAAGATGCGGATGAG–3?;and LBD42,5?-AAT-GGATCAAATCCGCAGAC-3?and5?-GAACTTGGGAGT-GCCACAT-3?.Primers to At5g63080were MDC12.4–1,5?-GCCATTGGAGGAGAAGCATC-3?and MDC12.4–2,5?-TTTCCAGCCATCGTGTCATA-3?.

Sequence Alignment and Block Analysis

Database searches were performed using TBLASTN (https://www.wendangku.net/doc/be16654582.html,/BLAST/).Protein sequences from each gene were aligned using AlignX program from Vector NTI suite(InforMax,Bethesda,MD).Alignments were done using the LOB sequence as the selected profile with a gap opening penalty of10and a gap extension penalty of0.1.The aligned sequences were shaded using MacBoxshade(http://www.isrec.isb-sib.ch/sib-isrec/ boxshade/MacBoxshade/)in an Encapsulated PostScript output.Conserved blocks were predicted by BlockMaker (https://www.wendangku.net/doc/be16654582.html,/)using the Motif algorithm and all class I or class II sequences as input.Secondary structure predictions were performed with NNPredict (https://www.wendangku.net/doc/be16654582.html,/?nomi/nnpredict; Kneller et al.,1990)and COILS(http://www.ch.embnet. org/software/COILS_form.html;Lupas et al.,1991)pro-grams.COILS parameters used the MTIDK matrix and a 2.5-fold weighting of positions a and d.A coiled coil of30 amino acids in length was predicted(?95%probability)in LOB with window sizes of14,21,and28. ACKNOWLEDGMENTS

We thank Mary Byrne,Elizabeth Bray and Linda Walling for comments on the manuscript,Janena Williams and Rob

The Arabidopsis LATERAL ORGAN BOUNDARIES Domain Gene Family

Lennox for assistance with plant growth,Catherine Bushell for help with RT-PCR,and members of the Springer labo-ratory for helpful discussions.We also thank the Arabidop-sis Biological Resource Center and the Kazusa DNA Re-search Institute for supplying cDNA clones and the Arabidopsis Knock-Out Facility for identifying the lob-2 allele.

Received October9,2001;returned for revision November 8,2001;accepted January7,2002.

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