Ahlquist Membrane compartments & Virus RNA Repliction factories

Organelle-Like Membrane Compartmentalization of Positive-Strand RNA Virus Replication Factories

Johan A.den Boon 1and Paul Ahlquist 1,2

Institute for Molecular Virology and 2Howard Hughes Medical Institute,University of Wisconsin-Madison,Madison,Wisconsin 53706;email:jdenboon@https://www.360docs.net/doc/3711471548.html,,ahlquist@https://www.360docs.net/doc/3711471548.html,

Annu.Rev.Microbiol.2010.64:241–56The Annual Review of Microbiology is online at https://www.360docs.net/doc/3711471548.html,

This article’s doi:

10.1146/annurev.micro.112408.134012Copyright c

0066-4227/10/1013-0241$20.00

Key Words

RNA replication complex,membrane association,EM tomography,spherule,vesicle

Abstract

Positive-strand RNA virus genome replication is invariably associated with extensively rearranged intracellular membranes.Recent biochemi-cal and electron microscopy analyses,including three-dimensional elec-tron microscope tomographic imaging,have fundamentally advanced our understanding of the ultrastructure and function of organelle-like RNA replication factories.Notably,for a range of positive-strand RNA viruses embodying many major differences,independent studies have revealed multiple common principles.These principles include that RNA replication often occurs inside numerous virus-induced vesicles invaginated or otherwise elaborated from a continuous,often endoplas-mic reticulum-derived membrane network.Where analyzed,each such vesicle typically contains only one or a few genome replication interme-diates in conjunction with many copies of viral nonstructural proteins.In addition,these genome replication compartments often are closely associated with sites of virion assembly and budding.Our understand-ing of these complexes is growing,providing substantial new insights into the organization,coordination,and potential control of crucial processes in virus replication.

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A n n u . R e v . M i c r o b i o l . 2010.64:241-256. D o w n l o a d e d f r o m w w w .a n n u a l r e v i e w s .o r g b y C h i n a A g r i c u l t u r a l U n i v e r s i t y o n 11/23/11. F o r p e r s o n a l u s e o n l y .

Positive-strand RNA virus:a virus with single-stranded genomic RNA of mRNA polarity,

immediately available as a template for translation of viral proteins

SARS:severe acute respiratory syndrome RNA replication complex:a complex of viral proteins with enzymatic function to copy RNA from an RNA template BMV:Brome mosaic virus

Contents

INTRODUCTION (242)

RNA REPLICATION COMPLEX ULTRASTRUCTURE AND

ASSEMBLY.......................242Brome Mosaic Virus ...............242Flock House Virus.................244Dengue Virus......................246Severe Acute Respiratory

Syndrome Virus ................247Poliovirus . (248)

CONSERVED AND DISTINCT FEATURES OF RNA

REPLICATION COMPLEXES...249Replication Complex Ultrastructure and Stoichiometry ..............249Coupled RNA Replication and

Virion Assembly................250EMERGING AND FUTURE

DIRECTIONS....................

250

INTRODUCTION

The positive-strand RNA viruses are the largest of the seven different genetic classes of viruses and include many pathogens of considerable medical and economic concern.Examples include hepatitis C virus (HCV),severe acute respiratory syndrome (SARS)virus,West Nile virus,poliovirus,and many economically im-portant animal and plant viruses.The genomes of these viruses are single-stranded RNAs of sense polarity that,upon virion entry and dis-assembly,function as mRNAs to translate the viral proteins.The initial translation products invariably include the viral RNA replication proteins,which then recruit the same incoming viral genome as a template for replication by an RNA-dependent RNA polymerase,usually assisted by other virus-encoded functions,such as RNA helicase and 5 capping/methylation activities.The genomic RNA is ?rst copied into a complementary negative-strand RNA,which is subsequently used as a template

for the production of large amounts of new positive-strand RNAs.

For all well-studied positive-strand RNA viruses,these genome replication events occur on speci?c intracellular membranes (1,21,57,63,68,84).However,many questions remain about the nature and function of this mem-brane association.This review highlights recent advances that collectively reveal that positive-strand RNA viruses rearrange cell membranes to produce sophisticated,organelle-like com-partments that scaffold,protect,and coordinate multiple facets of genome replication,expres-sion,and packaging.We regret that space con-straints preclude reviewing all the exciting work in this area.

RNA REPLICATION

COMPLEX ULTRASTRUCTURE AND ASSEMBLY

Below,we ?rst describe ultrastructure and as-sembly studies of the membrane-associated RNA replication complexes from a wide spec-trum of well-studied positive-strand RNA viruses,including viruses with single or multi-ple component genomes,enveloped or nonen-veloped virions,and many other varied features (Figure 1).Later sections compare and contrast these cases to further discuss emerging com-mon principles and their mechanistic and prac-tical implications.

Brome Mosaic Virus

Brome mosaic virus (BMV)is the type member of the plant bromoviruses in the alphavirus-like superfamily.BMV encodes two RNA replica-tion proteins,1a and 2a Pol (Figure 1a ).2a pol is the viral RNA-dependent RNA polymerase;1a provides 5 RNA capping and RNA NTPase/helicase functions essential for productive RNA synthesis (2,3,46,105).Most aspects of BMV replication can be reconstituted in the yeast Sac-charomyces cerevisiae by plasmid-based expres-sion of the viral proteins and genomic RNAs (30,35,37,48),and many features of BMV

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Viral RNA

cyto

Nuc

100 nm

ERL

CF ERL

ERL

Nuc

cyto

250 nm

Outer membrane

Spherules

100 nm

25 nm 25 nm Cytoplasm

Mitochondrial outer membrane

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DENV:dengue virus VP:vesicle packet CM:convoluted membrane

virus replication complex (Figure 3b–d ).Bio-chemical and molecular genetic approaches,including stoichiometry analysis,were used to complement the imaging.

Despite marked differences in hosts,genomes,replication factors,and sites,the results paralleled many ?ndings from the prior studies of BMV RNA replication complexes (47).Immunogold labeling showed that newly synthesized BrUTP-labeled viral RNA and protein A accumulated almost exclusively inside FHV replication vesicles.Each com-partment contained,on average,one or two genome replication intermediates.Like BMV,FHV replication complexes exported progeny positive-strand genomes to the cytoplasm for translation and encapsidation but retained negative-strand RNA intermediates.Such compartmentalization presumably helps to protect the virus from dsRNA-activated host defenses.Similar to the high copy number of 1a proteins in BMV spherules (Figure 2d ),each replication vesicle contained ～100copies of transmembrane,self-interacting protein A,a number suf?cient to form a full protein A shell lining the vesicle membrane (Figure 3e ).In addition,three-dimensional tomographic imaging resolved many crucial questions aris-ing from the limitations of two-dimensional imaging of random EM sections.Prominent among these questions was whether FHV repli-cation vesicles remained attached to or budded from the outer mitochondrial membrane,which has major mechanistic implications for genome synthesis and release.For FHV and BMV,traditional two-dimensional EM images revealed that a fraction of replication vesicles were invaginations of the parent mitochon-drial or ER membranes,retaining a necked connection between the vesicle interior and the cytosol that would allow ribonucleotide import and progeny RNA export (Figure 2c and Figure 3a ).However,by standard EM,most vesicles showed no such connection,which might re?ect either budding off or the vagaries of random sectioning.In contrast,three-dimensional EM tomography immedi-ately revealed that all FHV replication vesicles

were continuous with the outer mitochondrial membranes,such that each vesicle maintained an ～10-nm-diameter,neck-like connection with the cytoplasm (Figure 3b–d ),i.e.,a structure similar to a budding (but never budded)retrovirus virion (Figure 3e ).

Dengue Virus

Dengue virus (DENV)is a member of the Flaviviridae ,a family of viruses of consider-able medical importance that also includes hep-atitis C virus (HCV)and yellow fever virus.Flaviviruses are enveloped viruses with a sin-gle positive-strand genomic RNA (Figure 1a )(8,53,54).The ?avivirus genome is trans-lated into a single polyprotein precursor that is co-and posttranslationally cleaved into three structural viral proteins and seven nonstructural (NS)proteins required for RNA replication.These NS proteins include NS5,the RNA-dependent RNA polymerase and RNA capping enzyme (26,108),and NS3,with RNA heli-case/NTPase activity (104)and protease activ-ity responsible for viral polyprotein processing (7,27).NS2A,NS4A,and NS4B all have inte-gral membrane-spanning domains (59,62,64).Like other ?avivirus infections,DENV in-fection induces several distinct ER-derived membrane structures,including vesicle pack-ets (VPs),convoluted membranes (CMs),and membranes associated with virion assembly and budding (Figure 4a ,c )(31,58,107).VPs,which comprise multiple ～90-nm vesicles within a bounding ER membrane,are the sites of DENV RNA replication,based on their label-ing for multiple NS proteins,double-stranded RNA,and nascent RNA (58).CMs contain replicase proteins but no dsRNA and are pro-posed sites for production,processing,and stor-age of NS proteins and lipids for replication complex assembly (58,107).

Recent EM tomography studies by Bartenschlager and colleagues (107)provided high-resolution three-dimensional recon-structions of the different DENV-induced membrane structures.Strikingly,their analyses showed that the CM,VP,and even the sites of

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200 nm

Figure 4

Continuous ER-derived membranous networks in dengue virus (DENV)-infected convoluted membranes,vesicles,and tubular structures form a continuous network membranes.(b )Three-dimensional tomographic reconstruction of the membranes showing cytosol-exposed membrane surfaces and the ER lumen.(c ,d )Arrays of cisternae with connections to virus-induced vesicles (white arrow ).Abbreviations:CM,membrane;ER,endoplasmic reticulum;Ve,vesicular membranes;T,tubular membranes.Reference 107.)

III

I II III

50 nm

I II

Vesicle outer membrane Vesicle inner membrane Connection to ER stack Figure5

Membranous interconnected network of severe acute respiratory syndrome (SARS)virus-induced double-membrane vesicles.Electron microscope tomography-based,three-dimensional surface-rendered model of membrane rearrangements in SARS virus-infected Vero E6cells.Interconnected double-membrane vesicles with outer membranes,inner membranes,and their connection to an endoplasmic reticulum(ER)stack colored as shown in the

The PV genome (Figure 1a )expresses a single polyprotein whose P2-P3region encodes the replication proteins,includ-ing the three-dimensional RNA-dependent RNA polymerase,the 3B/VPg protein primer of RNA synthesis,the 2C NTPase,and other functions required for RNA replication.Domains in 2B,2C,and 3A (29,94,95)con-trol membrane association of the RNA replica-tion proteins,which assemble into a replication complex through multiple interactions (111).PV reorganizes ER,Golgi,and lysosomal membranes into clusters of 50-to 500-nm vesi-cles that are associated with RNA replication (Figure 6a )(11,25,85).Expressing PV 2BC or 2C proteins is suf?cient to induce sim-ilar membrane rearrangements (18).PV in-duction of these vesicles has been linked to COPII-dependent vesicle traf?cking (83)and may be assisted by PV activation of cellular Arf GTPases that modulate membrane traf?cking (10).In addition,the PV-induced vesicles are double-membrane bound and have autophago-somal characteristics (36,85,91,93).

The large size and double-membrane char-acter of PV replication vesicles appear similar to coronavirus DMVs.However,it is unclear how the organization of RNA replication in associa-tion with PV DMVs might relate to coronavirus DMVs.When isolated from infected cells,the PV-induced vesicle clusters have a rosette-like appearance (Figure 6b )(24).In these prepara-tions,immunogold labeling localizes viral RNA replication factors to the exposed surface of the vesicles,in the center of the rosettes where the vesicles cluster (11).

CONSERVED AND DISTINCT FEATURES OF RNA

REPLICATION COMPLEXES Replication Complex Ultrastructure and Stoichiometry

A common theme of nearly all studies above is the occurrence of viral RNA synthesis in-side virus-induced vesicle compartments.In particular,the membrane-bound replication

a b

100 nm

Figure 6

Poliovirus (PV)-induced vesicle clusters.(a )Electron microscope (EM)image of vesicular membrane rearrangements in PV-infected cells.(b )EM image of extracted vesicle clusters showing a typical rosette-like arrangement.(Adapted from References 85and 24.)

complexes of BMV,FHV,and ?aviviruses bear striking resemblances,including ～10-nm-diameter necked connections to the cytoplasm,one or a few RNA replication intermediates per vesicle,and one to a few hundred viral repli-cation protein copies per vesicle (47,77,86,107).Similar vesicular invaginations are asso-ciated with RNA replication by many other positive-strand RNA viruses (28,34).SARS coronavirus RNA synthesis also appears to oc-cur inside de?ned vesicles (45).Studies with bromoviruses,?aviviruses,and coronaviruses show that these membrane-associated struc-tures provide a nuclease-resistant environment for viral RNAs (65,77,86,88,99).The vary-ing sizes of FHV,BMV,DENV,and SARS virus–induced replication vesicles (～50,70,90,and 200–300nm,respectively)are roughly cor-related with the sizes of the respective viral genome components,which range from 1.5–3kb to 30kb,respectively.

SARS coronavirus DMVs were distin-guished from the other replication vesicles above in that they lacked a visible membrane opening between the vesicle interior and cy-toplasm (45).As noted above,ribonucleotide and product RNA transport might be mediated by proteinaceous channels.Such a possibility is consistent with the unusually large complement of coronavirus replication proteins (Figure 1b ),including multiple proteins with membrane-spanning domains (33,70,71).A possible

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precedent for a membrane-spanning viral chan-nel associated with RNA export may be pro-vided by picornavirus capsid protein VP4(19).

Coupled RNA Replication and Virion Assembly

The DENV and SARS virus EM tomography studies revealed that RNA replication and virion assembly and/or budding are closely coordinated within the same continuous membrane networks (45,107).Multiple reports provide evidence for coupling of RNA replication and virion assembly by other positive-strand RNA viruses.FHV coat protein must be synthesized from replicable RNA2to effectively package both FHV genomic RNAs (102),and EM tomography showed that FHV virions accumulate in arrays in close proximity to mitochondria bearing FHV RNA replica-tion vesicles (50).PV RNA replicons must be actively replicated to be encapsidated (69).Moreover,Kirkegaard and colleagues (36,43,93)have outlined elegant pathways by which RNA replication-associated PV DMVs,gener-ated by exploitation of cellular autophagy,could facilitate the export of progeny virions without cell lysis,enabling prolonged productive infec-tion.BMV virion assembly is likewise linked to active replication of the genomic RNAs (4–6).

EMERGING AND

FUTURE DIRECTIONS

As well as providing dramatic insights,the results on positive-strand RNA virus replica-tion complexes discussed above pose valuable new questions and opportunities for further re-search and development.Here we discuss a few of many such points.

One important set of questions in this ?eld is how viral replication factors target,bind,and rearrange speci?c membranes.As noted above,FHV protein A is targeted to mito-chondrial outer membranes by an N-terminal transmembrane domain similar to those of cellular proteins of the outer mitochondrial membrane (60).RNA replication proteins

of some other positive-strand RNA viruses,including ?aviviruses and coronaviruses,also encode transmembrane domains,but many do not.One alternative emerging theme is the use of amphipathic helices that mediate peripheral association with one lea?et of lipid bilayers.Examples of positive-strand RNA virus replication proteins with membrane-associating amphipathic helices include the N terminus of picornavirus 2C protein,NS4A of DENV and the related Kunjin West Nile virus (62,82),NS5A of HCV and related pestiviruses (12),nsp1of the BMV-related alphavirus Semliki Forest virus (89),and the N-proximal capping domain of BMV 1a (55).Picornavirus 2C,?avivirus NS4A,and BMV 1a all have been implicated in inducing membrane rearrangements (62,82,86,96).Mutational analysis of BMV 1a’s amphipathic helix shows that it,or its interaction with membranes,acts as a molecular switch to differentially control multiple 1a replication functions,including invagination of membrane spherules (55).

A related issue concerns the pathways by which membrane rearrangements associated with positive-strand RNA virus genome repli-cation arise.For example,intermediate states in retrovirus virion envelopment and budding are readily visualized by EM (44,67).However,for the viruses discussed above,similar intermedi-ates between normal cell membranes and the often large and complex RNA replication com-plexes have not been reported,despite searches of the relevant images (45,47).Although this suggests that the relevant membrane rearrange-ments are rapid,identifying intermediates will be an important step in resolving the relative roles of membrane folding,?ssion,fusion,and autophagy in forming the membrane complexes used by various viruses.For DENV and perhaps coronaviruses,CM may provide a link to such intermediates (45,107).

In addition to fundamental mechanistic issues,the emergence of common principles in replication complex ultrastructure offers opportunities for developing broad-spectrum antiviral controls.In keeping with the need to assemble replication complexes from multiple

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protein factors,often in high copy number,one control opportunity might arise from common dependencies of RNA replication on host chaperones including Hsp40,Hsp60,Hsp70,and/or Hsp90.Such chaperone dependency has been demonstrated,for example,for RNA replication by BMV (98),FHV (14,39,106),coronaviruses (66),and tombusviruses (87).In addition to other effects of chaperone inhibitors on viruses,the established value of chaperone inhibitors in cancer therapy (74)provides a clinical precedent for potential antiviral use.Other valuable opportunities for potentially broad antiviral approaches may arise from dependencies of membrane-associated RNA replication on general and speci?c lipid syn-thesis and membrane lipid composition (32,42,51,52,73,109).Further advances on the assembly,structure,and function of replication complexes appear certain to open additional avenues for virus control through targeting both viral and cellular factors.

SUMMARY POINTS

1.Genome replication by positive-strand RNA viruses occurs in association with mem-brane rearrangements.Viral RNA synthesis often occurs inside novel,infection-induced vesicles that retain negative-strand RNA intermediates while exporting progeny positive-strand RNA genomes to the cytoplasm.

2.These membrane compartments concentrate and sequester viral replication factors and templates,coordinate replication steps,and appear to protect RNA replication interme-diates from dsRNA-activated host defense responses.

3.For many viruses,the RNA replication vesicles are invaginations of ER or organellar membranes,whose necked opening to the cytoplasm provides a channel for ribonu-cleotide import and product RNA export.How the contents of apparently closed coron-avirus double-membrane replication vesicles are exchanged with the cytosol remains to be established.

4.The replication vesicles of at least some viruses appear to be lined by a capsid-like shell of many copies of a self-interacting,membrane-bound viral replication protein.Although strictly intracellular,these replication complexes have multiple similarities to retrovirus and dsRNA virus virions,suggesting evolutionary links between virus classes.

5.For enveloped and nonenveloped viruses,virion assembly sites are positioned in direct association with the membrane-bound genome replication complexes,implying close coordination of genome synthesis and packaging.

DISCLOSURE STATEMENT

The authors are not aware of any af?liations,memberships,funding,or ?nancial holdings that might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS

We are grateful for the generosity of a number of authors and publishers in allowing us to use and adapt their original published illustrations.Research in the authors’laboratory was funded by the National Institutes of Health.P.A.is an Investigator of the Howard Hughes Medical Institute.

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256den Boon

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Annual Review of Microbiology Volume 64,2010

Contents

Conversations with a Psychiatrist

L.Nicholas Ornston p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1Vaccines to Prevent Infections by Oncoviruses

John T .Schiller and Douglas R.Lowy p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 23T onB-Dependent T ransporters:Regulation,Structure,and Function

Nicholas Noinaj,Maude Guillier,Travis J.Barnard,and Susan K.Buchanan p p p p p p p p p p p 43Genomes in Con?ict:Maintaining Genome Integrity During Virus Infection

Matthew D.Weitzman,Caroline E.Lilley,and Mira S.Chaurushiya p p p p p p p p p p p p p p p p p p p p 61DNA Viruses:The Really Big Ones (Giruses)

James L.V an Etten,Leslie https://www.360docs.net/doc/3711471548.html,ne,and David D.Dunigan p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 83Signaling Mechanisms of HAMP Domains in Chemoreceptors and Sensor Kinases

John S.Parkinson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 101Viruses,microRNAs,and Host Interactions

Rebecca L.Skalsky and Bryan R.Cullen p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 123Basis of Virulence in Community-Associated Methicillin-Resistant Staphylococcus aureus

Michael Otto p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 143Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles

Adam Kulp and Meta J.Kuehn p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 163Structure,Function,and Evolution of Linear Replicons in Borrelia

George Chaconas and Kerri Kobryn p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 185Intracellular Lifestyles and Immune Evasion Strategies of Uropathogenic Escherichia coli

David A.Hunstad and Sheryl S.Justice p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 203Bacterial Shape:T wo-Dimensional Questions and Possibilities

Kevin D.Y oung p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 223

Organelle-Like Membrane Compartmentalization of Positive-Strand RNA Virus Replication Factories

Johan A.den Boon and Paul Ahlquist p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 241Noise and Robustness in Prokaryotic Regulatory Networks Rafael Silva-Rocha and V′?ctor de Lorenzo p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 257Genetic Diversity among Offspring from Archived Salmonella enterica ssp.enterica Serovar T yphimurium (Demerec Collection):In Search of Survival Strategies

Abraham Eisenstark p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 277

Letting Sleeping dos Lie:Does Dormancy Play a Role in T uberculosis?

Michael C.Chao and Eric J.Rubin p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 293Mechanosensitive Channels in Microbes

Ching Kung,Boris Martinac,and Sergei Sukharev p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 313Mycobacteriophages:Genes and Genomes

Graham F .Hatfull p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 331Persister Cells

Kim Lewis p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 357Use of Fluorescence Microscopy to Study Intracellular Signaling in Bacteria

David Kentner and Victor Sourjik p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 373Bacterial Microcompartments

Cheryl A.Kerfeld,Sabine Heinhorst,and Gordon C.Cannon p p p p p p p p p p p p p p p p p p p p p p p p p p p p 391Mitochondrion-Related Organelles in Eukaryotic Protists

April M.Shi?ett and Patricia J.Johnson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 409Stealth and Opportunism:Alternative Lifestyles of Species in the Fungal Genus Pneumocystis

Melanie T .Cushion and James R.Stringer p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 431How to Make a Living by Exhaling Methane

James G.Ferry p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 453CRISPR/Cas System and Its Role in Phage-Bacteria Interactions H′e l`e ne Deveau,Josiane E.Garneau,and Sylvain Moineau p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 475Molecular Insights into Burkholderia pseudomallei and Burkholderia mallei Pathogenesis

Edouard E.Galyov,Paul J.Brett,and David DeShazer p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 495Unique Centipede Mechanism of Mycoplasma Gliding

Makoto Miyata p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 519

Contents vii

Bacterial Sensor Kinases:Diversity in the Recognition of Environmental Signals Tino Krell,Jes ′us Lacal,Andreas Busch,Hortencia Silva-Jim′e nez,Mar′?a-Eugenia Guazzaroni,and Juan Luis Ramos p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 539Iron-Oxidizing Bacteria:An Environmental and Genomic Perspective

David Emerson,Emily J.Fleming,and Joyce M.McBeth p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 561Fungi,Hidden in Soil or Up in the Air:Light Makes a Difference

Julio Rodriguez-Romero,Maren Hedtke,Christian Kastner,Sylvia M ¨

uller,and Reinhard Fischer p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 585

Index

Cumulative Index of Contributing Authors,Volumes 60–64p p p p p p p p p p p p p p p p p p p p p p p p p p p 611Errata

An online log of corrections to Annual Review of Microbiology articles may be found at https://www.360docs.net/doc/3711471548.html,/

viii Contents