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Taken together, these studiesprovide a compelling model for novelbacteriophage tubulins. With an overallfilament morphology similar to TubZ(and ultimately to F-actin) [9], 201f2-1PhuZ and c-st TubZ seem importantfor forming a cytoskeleton withintheir host to organize the replicationof their large genomes and to maximizetheir reproduction (Figure 1). Yet, manyquestions remain. As many of thein vivo experiments in the PhuZ studywere done with overproduced protein,it will be important to assess the roleof native PhuZ levels during theinfection process, whether a phuZnull phage has significant defects,and whether cytoskeletal structuresfrom native expression can be detectedin situ. It will also be interesting tosee how PhuZ interacts with otherphage or host factors that mightregulate phage DNA organization orPhuZ assembly. Indeed, Oliva et al. [10]found a gene adjacent to tubZ in phagec-st (tubY) that encodes a potentmodulator of in vitro TubZ assembly.Finally, onemajor question iswhy thesephages carry their own cytoskeletaltool with them, rather than make useof the host cell cytoskeleton as doeukaryotic viruses. One possibilityis that large phage genomes requiremore stringent organization of theirDNA and using a host factor forthis purpose is too risky for thephage. Future studies will further

illuminate this exciting new areaof phage biology.

References1. Wickstead, B., and Gull, K. (2011). The

evolution of the cytoskeleton. J. Cell Biol. 194,513–525.

2. Ingerson-Mahar, M., and Gitai, Z. (2012). Agrowing family: The expanding universe of thebacterial cytoskeleton. FEMS Microbiol. Rev.36, 256–266.

3. Erickson, H.P., Anderson, D.E., and Osawa, M.(2010). FtsZ in bacterial cytokinesis:cytoskeleton and force generator all in one.Microbiol. Mol. Biol. Rev. 74, 504–528.

4. Gerdes, K., Howard, M., and Szardenings, F.(2010). Pushing and pulling in prokaryotic DNAsegregation. Cell 141, 927–942.

5. Pilhofer, M., Ladinsky, M.S., McDowall, A.W.,Petroni, G., and Jensen, G.J. (2011).Microtubules in bacteria: Ancient tubulins builda five-protofilament homolog of the eukaryoticcytoskeleton. PLoS Biol. 9, e1001213.

6. Bravo, A., and Salas, M. (1997). Initiation ofbacteriophage f29 DNA replication in vivo:assembly of a membrane-associatedmultiprotein complex. J. Mol. Biol. 269,102–112.

7. Bravo, A., and Salas, M. (1998). Polymerizationof bacteriophage f29 replication protein p1into protofilament sheets. EMBO J. 17,6096–6105.

8. Derman, A.I., Becker, E.C., Truong, B.D.,Fujioka, A., Tucey, T.M., Erb, M.L.,Patterson, P.C., and Pogliano, J. (2009).Phylogenetic analysis identifies manyuncharacterized actin-like proteins (Alps) inbacteria: Regulated polymerization, dynamicinstability and treadmilling in Alp7A. Mol.Microbiol. 73, 534–552.

9. Kraemer, J.A., Erb, M.L., Waddling, C.A.,Montabana, E.A., Zehr, E.A., Wang, H.,Nguyen, K., Pham, D.S., Agard, D.A., andPogliano, J. (2012). A phage tubulin assemblesdynamic filaments by an atypical mechanism tocenter viral DNA within the host cell. Cell 149,1488–1499.

10. Oliva, M.A., Martin-Galiano, A.J., Sakaguchi, Y.,and Andreu, J.M. (2012). Tubulin homologTubZ in a phage-encoded partition system.

Proc. Natl. Acad. Sci. USA 109,7711–7716.

11. Sakaguchi, Y., Hayashi, T., Kurokawa, K.,Nakayama, K., Oshima, K., Fujinaga, Y.,Ohnishi, M., Ohtsubo, E., Hattori, M., andOguma, K. (2005). The genome sequence ofClostridium botulinum type Cneurotoxin-converting phage and themolecular mechanisms of unstable lysogeny.Proc. Natl. Acad. Sci. USA 102,17472–17477.

12. Ni, L., Xu, W., Kumaraswami, M., andSchumacher, M.A. (2010). Plasmid proteinTubR uses a distinct mode of HTH-DNA bindingand recruits the prokaryotic tubulin homologTubZ to effect DNA partition. Proc. Natl. Acad.Sci. USA 107, 11763–11768.

13. Bravo, A., Illana, B., and Salas, M. (2000).Compartmentalization of phage f29 DNAreplication: Interaction between the primerterminal protein and the membrane-associatedprotein p1. EMBO J. 19, 5575–5584.

14. Munoz-Espin, D., Holguera, I., Ballesteros-Plaza, D., Carballido-Lopez, R., and Salas, M.(2010). Viral terminal protein directs earlyorganization of phage DNA replication at thebacterial nucleoid. Proc. Natl. Acad. Sci. USA107, 16548–16553.

15. Kamtekar, S., Berman, A.J., Wang, J.,Lazaro, J.M., de Vega, M., Blanco, L., Salas, M.,and Steitz, T.A. (2006). The f29 DNApolymerase:protein-primer structure suggestsa model for the initiation to elongationtransition. EMBO J. 25, 1335–1343.

16. Gonzalez-Huici, V., Alcorlo, M., Salas, M., andHermoso, J.M. (2004). Phage f29 proteins p1and p17 are required for efficient binding ofarchitectural protein p6 to viral DNA in vivo.J. Bacteriol. 186, 8401–8406.

Department of Microbiology and MolecularGenetics, University of Texas Medical Schoolat Houston, 6431 Fannin Street, Houston,TX 77030, USA.E-mail: Daniel.P.Haeusser@uth.tmc.edu,William.Margolin@uth.tmc.edu

http://dx.doi.org/10.1016/j.cub.2012.07.027

Programmed GenomeRearrangements: In Lampreys,All Cells Are Not Equal

Howcan organisms silence deleterious gene loci? A recent study has shed lighton a very brute mechanism in a jawless vertebrate: the irreversible deletion ofmassive chunks of genomic DNA.

Marie Semon, Michael Schubert,and Vincent Laudet*

It is commonly accepted that,excepting the combinatorialdiversity of immune cells, cells fromthe same individual share the samegenome. However, this dogma hasbeen challenged by recent workdemonstrating that the cells of agiven organism represent a

mosaic of genomes with randomabnormalities introduced, forexample, during aging [1,2]. Incontrast, clear cases of programmedgenomic rearrangements, rangingfrom intra-chromosomal changes tothe loss of complete chromosomes,albeit known for a long time, arestill relatively rare. For example, in1887 Boveri described the loss ofchromatin during the development

of the parasitic nematode wormAscaris megalocephala [3]. Thispioneering study was followed bysimilar descriptions in otherparasitic nematodes, and also incopepods (crustaceans), dipteranflies (insects), hagfish (agnathanvertebrates), zebra finches(birds), bandicoots (marsupials)and even ciliates (protists) [4–12].A particular case of specific

genomic reorganization in animalsis the so-called developmentallyprogrammed genomerearrangement (PGR) leading tothe elimination of portions ofchromosomes (chromatindiminution) or the loss of entirechromosomes (chromosomeelimination) during embryonicdevelopment [4]. PGR thus describesthe loss of DNA in somatic cells

BlastulaCleavagestage

Gastrula Larva

Mid-blastulatransition

(MBT)

Egg Elongatingembryo

A CProgrammed

genomerearrangements

(PGR)

A B CGermline

Soma

A B C

A B C

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Figure 1. Programmed genome rearrangement (PGR) in lampreys.

Programmed genome rearrangement (PGR) in lampreys probably coincides with the initiationof zygotic gene expression at the mid-blastula transition (MBT). The PGR process does notaffect germline cells, but removes potentially deleterious DNA sequences from somatic cells.Both repetitive (black boxes) and single-copy loci (colored boxes) undergo PGR in lampreys.The representations of lamprey development are from [19] and correspond to the lampreyLampetra reissneri.

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during early development, producinga somatic genome that is differentfrom the germline genome, which isnot modified in this process [4]. Thefirst thorough genomic analysis of thisprocess in a vertebrate, carried outby Smith et al. [13], is presented inthis issue of Current Biology.

Following a study published bythe same group in 2009 [14], wherethey first discovered that the sealamprey (Petromyzon marinus) [15]undergoes PGR during earlydevelopment, Smith et al. [13] nowdescribe in much greater detail thegenomic consequences of theserearrangements. Lampreys togetherwith hagfish form a monophyleticclade called the cyclostomes (jawlessvertebrates), which constitutes thesister clade of the gnathostome (jawed)vertebrates [16]. With a combinationof microarray- and high throughputsequencing-based approaches, theyestablished a list of genomic regionslost during PGR. In a first step, usinga customized microarray, theyidentified sequences enriched in thesea lamprey male germline relative tomale adult tissues. This approach alsoallowed an estimate of the percentageof genomic sequences removed inadult tissues (13%), which is inaccordance with previous estimates(20%) [14]. Themicroarray analysis wascomplemented with sequence datacovering 10% of the genome of themale germline, which was comparedto the sequences obtained as part ofthe lamprey genome sequencingproject from the liver of a female sealamprey [13]. The overall results from

these genome-scale comparisonslend further support to the idea thatthe lamprey genome undergoessevere PGR.

Importantly, this study offers newinsights into the nature of thesequences subjected to deletion. Asa matter of fact, in the sea lamprey,both repetitive elements [14] andsingle-copy, protein-coding genes aresubject to PGR-dependent deletion[13]. This finding contrasts withprevious reports on PGR that chieflyreported the loss of repetitive DNA,such as satellite sequences [5]. Itremains to be established whether theloss of specific genomic regions in thesea lamprey is a secondary effect dueto the excision of neighboring repetitiveDNA or whether amechanism exists fortargeting unique genomic sequencesfor deletion.

Previous analyses in hagfish, thesister group of lampreys, haverevealed both chromatin diminutionand chromosome elimination withrepetitive elements generallyaccounting for the majority of thelost DNA [9]. The fact that PGRseems to occur in both cyclostomelineages raises the possibility thatthis mechanism is conserved withinthis lineage. Given the paucity ofdata about the occurrence of PGRin other vertebrates, it remains tobe established whether PGR is anancestral feature of all vertebratesor a derived feature that originatedin cyclostomes.

In their study, Smith et al. [13] alsofound that the deleted genes function intranscriptional programs regulating

germline versus somatic cell fates. Itthus seems that in the sea lampreyone of the consequences of PGR isa functional limitation of somatic cellsrelative to the germline cells, which arenot subjected to PGR. Future studieswill need to address the question,whether the removed genes aredeleterious when expressed in somaticcells or simply dispensable fordevelopment and survival. Inaddition, the results indicate that, inlampreys, the germline is defined wellbefore the PGR event, which mightcoincide with the initiation of zygoticgene expression at the mid-blastulatransition [14] (Figure 1). In this context,it will be very important to assessthe mechanisms controlling PGR insea lampreys.Some clues about the possible

mechanisms underlying PGR comefrom unicellular eukaryotes. Indeed,ciliates represent a very powerfulmodel for studying the molecularmechanisms underlying genomicrearrangements. These protistsextensively remodel their genomesduring nuclear development, froma germline micronucleus to a somaticmacronucleus [12]. Intriguingly, whilethe removal of repetitive sequences inciliates is imprecise, certain genomicregions are specifically excised ina process involving a domesticatedtransposase [17]. The recognition ofthe regions to be removed involvesmaternal somatic non-coding RNAsthat protect zygotic DNA fromelimination [18]. Along the same lines,data from parasitic nematodes suggestthat maternal cytoplasmicdeterminants, probably containingRNA, play important roles in theprotection from chromatin diminution[4]. While PGR protection might thusbe a maternally controlled process, it isprobable that the removal of genomicDNA in the developing embryo mightwell be controlled independently ineach cell type or tissue. If this was thecase, it is conceivable that PGR doesnot target the same genomic loci indifferent cellular contexts.The findings by Smith et al. [13]

create a number of prospects forfurther investigations. For example,future studies need to assess howcomparable the genomicconsequences of chromatin diminutionare between the cells of a givenorganism, between sexes, and, moregenerally, between individuals anddifferent cyclostome species. Further,

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it will be important to analyze theeffects of the large-scale genomicrearrangements on global regulationof the transcriptome. These questionscan be addressed, for instance,by using the latest sequencingtechnologies. Moreover, the molecularmechanisms of this PGR phenomenonin lampreys need to be studied,including the developmental timing andmolecular components regulating bothDNA recognition and removal.

Taken together, we are just startingto unravel the biological significance ofPGR, with the most fundamentalquestions remaining to be answered:what could this mechanism, whichseems to be more widespread thaninitially anticipated, be used for andhow conserved is this process in allliving organisms? If PGR is indeedunderstood as an irreversiblemechanism of gene silencing, it mightbe pertinent to compare and contrastPGR with known reversiblemechanisms of gene silencing,including epigenetic modificationsof chromatin and DNA.

References1. Jacobs, K.B., Yeager, M., Zhou, W.,

Wacholder, S., Wang, Z., Rodriguez-Santiago, B., Hutchinson, A., Deng, X., Liu, C.,Horner, M.J., et al. (2012). Detectable clonal

mosaicism and its relationship to aging andcancer. Nat. Genet. 44, 651–658.

2. Laurie, C.C., Laurie, C.A., Rice, K.,Doheny, K.F., Zelnick, L.R., McHugh, C.P.,Ling, H., Hetrick, K.N., Pugh, E.W., Amos, C.,et al. (2012). Detectable clonal mosaicism frombirth to old age and its relationship to cancer.Nat. Genet. 44, 642–650.

3. Boveri, T. (1887). Uber Differenzierung derZellkerne wahrend der Furchung des Eiesvon Ascaris megalocephala. Anat. Anz. 2,688–693.

4. Kloc, M., and Zagrodzinska, B. (2001).Chromatin elimination: an oddity or a commonmechanism in differentiation and development?Differentiation 68, 84–91.

5. Muller, F., and Tobler, H. (2000). Chromatindiminution in the parasitic nematodes Ascarissuum and Parascaris univalens. Int. J. Parasitol.30, 391–399.

6. Nemetschke, L., Eberhardt, A.G., Hertzberg, H.,and Streit, A. (2010). Genetics, chromatindiminution, and sex chromosome evolution inthe parasitic nematode genus Strongyloides.Curr. Biol. 20, 1687–1696.

7. Beermann, S. (1959). Chromatin-diminution beiCopepoden. Chromosoma 10, 504–514.

8. Sanchez, L., and Perondini, A.L.P. (1999). Sexdetermination in sciarid flies: a model for thecontrol of differential X-chromosomeelimination. J. Theor. Biol. 197, 247–259.

9. Kohno, S., Kubota, S., and Nakai, Y. (1998).Chromatin diminution and chromosomeelimination in hagfish species. In The Biology ofHagfishes, J.M. Jorgensen, J.P. Lomholt,R.E. Weber, and H. Malte, eds. (London:Chapman and Hall), pp. 81–100.

10. Pigozzi, M.I., and Solari, A.J. (2005). Thegerm-line-restricted chromosome in the zebrafinch: recombination in females and eliminationin males. Chromosoma 114, 403–409.

11. Watson, C., Margan, S., and Johnston, P.(1998). Sex-chromosome elimination inthe bandicoot Isoodon macrourus using Y-linked markers. Cytogenet. Cell Genet. 81,54–59.

12. Prescott, D. (1994). The DNA of ciliatedprotozoa. Microbiol. Rev. 58, 233–267.

13. Smith, J.J., Baker, C., Eichler, E.E., andAmemiya, C.T. (2012). Genetic consequencesof programmed genome rearrangement. Curr.Biol. 22, 1524–1529.

14. Smith, J.J., Antonacci, F., Eichler, E.E., andAmemiya, C.T. (2009). Programmed loss ofmillions of base pairs from a vertebrategenome. Proc. Natl. Acad. Sci. USA 106,11212–11217.

15. Piavis, G.W. (1971). Embryology. In The Biologyof Lampreys, Volume 1 (London: AcademicPress), pp. 361–400.

16. Heimberg, A.M., Cowper-Sal-lari, R.,Semon, M., Donoghue, P.C., and Peterson, K.J.(2010). MicroRNAs reveal the interrelationshipsof hagfish, lampreys, and gnathostomesand the nature of the ancestral vertebrate.Proc. Natl. Acad. Sci. USA 107,19379–19383.

17. Chalker, D.L., and Yao, M.C. (2011). DNAelimination in ciliates: transposondomestication and genome surveillance. Annu.Rev. Genet. 45, 227–246.

18. Duharcourt, S., Lepere, G., and Meyer, E.(2009). Developmental genome rearrangementsin ciliates: a natural genomic subtractionmediated by non-coding transcripts. TrendsGenet. 25, 344–350.

19. Tahara, Y. (1988). Normal stages ofdevelopment in the lamprey, Lampetra reissneri(Dybowski). Zool. Sci. 5, 109–118.

Institut de Genomique Fonctionnelle de Lyon(UMR 5242 du CNRS, Ecole NormaleSuperieure de Lyon, Universite ClaudeBernard Lyon 1), Universite de Lyon, 46 Alleed’Italie, 69364 Lyon Cedex 07, France.*E-mail: Vincent.Laudet@ens-lyon.fr

http://dx.doi.org/10.1016/j.cub.2012.06.022

Actin Cytoskeleton: A Team Effortduring Actin Assembly

Two recent studies highlight how tandems of previously described actinnucleators collaborate to produce new actin filaments. One key player in thesecollaborations is formin, which appears to function as a modulator of filamentelongation.

Laurent Blanchoinand Alphee Michelot

The actin cytoskeleton of eukaryoticcells is characterized by numerousdifferent structures, each composed ofdynamic assemblies of actin filaments.These structures with their differentgeometric and mechanical propertiesare each tuned to perform particularcellular functions [1]. The first criticalstep towards the generation of a newactin structure is the targetednucleation of individual actin filamentsfrom a cytoplasmic pool of actinmonomers. In the cytoplasm,

nucleators are essential for generatingnew filaments because actinmonomers are buffered by profilinto inhibit spontaneous actin assembly.After nucleation, additional factors arerequired to spatially and temporallycontrol the elongation of actinfilaments [2].

Because our knowledge of theproteins involved in the nucleationof actin filaments has been limited formany years, it was naively believed thateach nucleator is uniquely implicatedin the generation of a particular typeof actin-filament structure. The firstactin nucleator to be discovered was

the Arp2/3 complex. This complexhas relatively similar biochemicalproperties in a variety of experimentalsystems tested so far, and itsconstituent proteins are conservedacross a wide range of organisms [3].For this reason, the Arp2/3 complexalone was often considered as theonly contributor to all branched actinnetworks in cells, such as those foundin lamellipodia or at sites ofclathrin-mediated endocytosis. Forminwas the second actin nucleator to bediscovered. Formin assemblesunbranched actin filaments, andtypically remains processivelyassociated with the fast-growing(barbed) end of the actin filament [3].Formins are implicated in the regulationof linear bundles of actin filaments,such as yeast cables, filopodialstructures or the contractile ring duringcytokinesis.Two important recent discoveries

[4,5] now challenge the concept thata distinct structure of actin filaments