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The gas vacuole was first observed in 1895, but details of this structure (gas vesicles) aswell as discovery of the other structures covered in this monograph (proteasomes, phycobilisomes,chlorosomes, carboxysomes and carboxysome-like inclusions, magnetosomes, intracytoplasmic membranes,membrane-bounded nucleoids, pirellulosomes, anammoxosomes and the cytoarchitecture of  spp.)awaited the availability of the transmission electron microscope and related technologies. Additionaladvancements in electron microscopy were required for the optimal visualization of some structures.

A growing number of proteases and peptidases have been identified that form large nanocompartmentalizedstructures in the cytosol, membrane, and extramembrane of cells. In archaea, these include the intracellularenergy-dependent proteasomes and the membrane-associated Lon protease as well as the intracellular energy-independenttetrahedral aminopeptidase (TET), tricorn peptidase (TRI), and PfpI-like proteases. Homologs of HtrA proteinsare also distributed in some archaea and may form nanocompartments that switch function from chaperone toprotease with increasing temperature. The location of these latter homologs remains to be determined.

The process of photosynthesis is initiated by the absorption of light energy by large arrays of pigmentsbound in an ordered fashion within protein complexes called antennas. These antennas transfer the absorbedenergy at almost 100% efficiency to the reaction centers that perform the photochemical electron transferreactions required for the conversion of the light energy into useful and storable chemical energy. Inprokaryotic cyanobacteria, eukaryotic red algae and cyanelles, the major antenna complex is called the phycobilisome,an extremely large (3–7 MDa) multi subunit complex found on the stromal side of the thylakoidmembrane. Phycobilisomes are assembled in an ordered sequence from similarly structured units that covalentlybind a variety of linear tetrapyrolle pigments called bilins. Phycobilisomes have a broad cross-sectionof absorption (500–680 nm) and mainly transfer the absorbed energy to photosystem II. Theycan, however, function as an antenna of photosystem I, and their composition can be altered as a resultof changes in the environmental light quality. The phycobilisome is structurally and functionally differentfrom other classes of photosynthetic antenna complexes. In this review, we will describe the importantstructural and functional characteristics of the phycobilisome complex and its components, especially withrespect to its assembly and disassembly.

Chlorosomes are the light-harvesting antenna organelles found in two groups of bacteria, thegreen sulfur bacteria and the green filamentous bacteria, collectively known as photosynthetic greenbacteria. Chlorosomes consist mostly of aggregated bacteriochlorophyll (BChl) ,, or and are the largestantenna structures known. Unlike other light-harvesting antenna structures, the major antenna pigments(BChl , , or )form aggregates that do not require a protein scaffold. This is possible because these BChlspossess structural modifications that do not occur in other naturally occurring chlorophyll derivatives.These properties allow the formation of very large and efficient antennae that permit phototrophicgrowth at remarkably low light intensities. The BChl aggregates are enveloped in a monolayerprotein–lipid membrane with a high content of glycolipids. Chlorosomes also contain smallamounts of BChl bound to the CsmA protein, other protein speciesof mostly unknown function, carotenoids, and isoprenoid quinones. Chlorosomes from thermophilic greenbacteria also contain wax esters. Although very little is known about how chlorosomes are synthesizedby the cells, significant efforts have been devoted to understanding the structural organization andenergy transfer characteristics of the BChl aggregates in chlorosomes. This is in part because theseaggregates serve as models of self-assembling systems and their potential use as light-harvestingnanostructures in artificial photosystems. Recent progress in genetic manipulation of BChl , carotenoids, and chlorosome envelope proteins in green sulfur bacteriahas allowed a better understanding of how these components function in chlorosomes.

Gas vesicles are hollow proteinaceous structures of spindle or cylinder shape produced by many cyanobacteria,heterotrophic bacteria and Archaea. Because of their gas content, gas vesicles decrease the cell densityand provide neutral or even positive buoyancy to cells. The rigid wall is formed solely from protein andis freely permeable to gas molecules. A major constituent of the wall is the small hydrophobic proteinGvpA that is arranged along 4.5 nm wide ribs running perpendicular to the long axis of the gas vesicle.The surface tension at the hydrophobic inner surface excludes the formation of water droplets inside. A secondprotein, GvpC, is attached to the outside surface strengthening the structure, and five additional Gvp proteinsare present in minor amounts. Gas vesicle formation involves the expression of 10 to 14 gas vesicle protein() genes. Ten genes have beenidentified in the cyanobacterium , whereas 14 genes are found in halophilic Archaea. Gas-vesiculate microorganisms occurabundantly in aqueous environments, but recently, homologues of the genes have been also detected in sporulating soil bacteria such as and ,raising the question of additional functions of Gvp proteins.

Carboxysomes and related polyhedral bacterial inclusions are complex structures that are composedof a limited set of related proteins. The importance of these prokaryotic organelles as metabolicorganizers in autotrophs as well as heterotrophic bacteria is becoming much more apparent. The carboxysome,which is by far the best characterized representative of these inclusions, is found in a variety ofphylogenetically distant autotrophic bacteria and contains the central fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). The particle participates in theessential CO concentrating mechanism and is likely protecting RuBisCO from oxygen.By contrast, the functions of polyhedral inclusions in heterotrophic prokaryotes that have been experimentallyobserved or inferred from comparative genomic analyses are less well understood. This review summarizesthe current state of knowledge regarding structure, function and genetics of carboxysomes and related polyhedralmicrocompartments.

The ability of magnetotactic bacteria (MTB) to orient and migrate along magnetic field lines is basedon magnetosomes, which are membrane-enclosed intracellular crystals of a magnetic iron mineral. Thebiomineralization of magnetosomes is a process with genetic control over the accumulation of iron,the deposition of the magnetic crystal within a specific compartment, as well as their intracellularassembly and alignment into chain-like structures. Magnetite crystals produced by MTB have uniform species-specificmorphologies and sizes, which are mostly unknown from inorganic systems. In addition, magnetosome chainformation is an example of the highest structural level achievable in a prokaryotic cell. In thiswork, we give an overview of the biology of MTB and the structure and functions of bacterial magnetosomes.In addition we summarize the current knowledge of the physico-chemical and molecular genetic basis of magnetosomebiomineralization and chain formation.

A variety of prokaryotes increase their membrane surface area for energy transduction processesby developing an intracytoplasmic membrane (ICM), in the form of tubules, interconnected vesicles, and single,paired or stacked lamellae. Recent images of the ICM of the photosynthetic bacterium , obtained by atomic force microscopy, have provided the first submolecular surfaceviews of any complex multi-component membrane. These topographs revealed rows of dimeric core light-harvesting1 (LH1) (RC) complexes, interconnected by the peripheral light-harvesting 2 (LH2) complex, which also existedin separate clusters. In addition, polarized light spectroscopy demonstrated that this optimal functionalarrangement is extended into a long-range pattern of membrane organization. Functional insights providedby the detailed structures of the light-harvesting, RC and cytochrome complexes are also discussed, including how LH1 is organized to facilitate ubiquinone exchange. It wasshown that LH1-RC core structures are inserted initially into the cytoplasmic membrane, which upon additionof LH2, invaginates to form the ICM, with LH2 packing between rows of dimeric core complexes, and ultimatelyforming separate bulk LH2 clusters. The ICM of the ecologically important methanotrophs, and chemolithotrophicnitrifying bacteria that convert ammonia to nitrite, is also discussed. The recent determination of thecrystal structure of the major ICM protein, methane monooxygenase, and the complete genome sequence of , are providing further insights into the molecular detailsof both methane oxidation and utilization of the resulting methanol as a sole source of carbon andenergy.

Planctomycetes are peptidoglycan-less organisms that form a distinct phylum of domain Bacteria. The cells of all planctomycetes examined share a cell plan involving intracellularmembranes, in which the cytoplasm is divided into compartments. Planctomycetes in genera , and possess a pirellulosome compartment bounded by a single membrane and containing ribosome-likeparticles, but all planctomycetes examined possess a topologically equivalent compartment. In allplanctomycetes the nucleoid is enclosed by the pirellulosome membrane. The space between the pirellulosome'smembrane and the cytoplasmic membrane forms another planctomycete-characteristic compartment, the paryphoplasm.In , cells possess a membrane-bounded nucleoid,where the nucleoid is surrounded by an envelope comprising two apposed membranes, forming a ‘nuclearbody’ region within the pirellulosome, analogous to the structure of a eukaryotic nucleus. Planctomycetecompartmentalization may have functional roles in anaerobic ammonium-oxidizing anammox planctomycetes, wherethe anammoxosome harbours specialized enzymes and its envelope possesses unique ladderane lipids (discussedin detail elsewhere in this volume, Fuerst 2006, in this volume). Compartmentalized cells of members ofthe distinctive phylum , especially those of strains, form an exception to the prokaryote cell plan and have significantimplications for models for origins of the eukaryote nucleus.

Anammoxosomes are unique metabolically significant compartments of planctomycetes performing the process. These bacteria carry out aerobiconium idation, a chemolithotrophicand autotrophic metabolism. They comprise genera “Brocadia”,“Kuenenia” and “Scalindua”, mostly from wastewater treatment bioreactors or marineanaerobic habitats and none of which are yet in pure culture. Like cells of other planctomycetes, anammoxspecies possess a shared planctomycete cell plan involving a single-membrane-bounded pirellulosomecompartment containing a nucleoid as well as paryphoplasm surrounding the outer rim of the cell. Withinthe pirellulosome they possess another compartment, the anammoxosome, unique to anammox planctomycetes.The anammoxosome harbours an enzyme, hydrazine oxidoreductase, important for models of anammox. The anammoxosomeis wrapped in an envelope possessing cyclobutane-containing ladderane lipids which may confer impermeabilityto anammoxosome membranes. The ladderanes occur in both ether-linked and ester-linked forms. This envelopemay have specialized functions, for example, protection from toxic intermediates of anammox metabolism andproton gradient formation for bioenergetics. The anammoxosome is important for models of anaerobic ammoniumoxidation. It has other unusual features related to cell biology, since within the anammoxosome tubulesoccur which may form distinct arrangements suggesting a cytoskeletal function, and the nucleoid isoften in contact with the anammoxosome envelope.