Gas vesicles

Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon

Halobacterium species display a variety of responses to light, including phototrophic growth, phototactic behavior, and photoprotective mechanisms. The complete genome sequence of Halobacterium species NRC-1 (Proc Natl Acad Sci USA 97: 12176-12181, 2000), coupled with the availability of a battery of methods for its analysis makes this an ideal model system for studying photobiology among the archaea. Here, we review: (1) the structure of the 2.57 Mbp Halobacterium NRC-1 genome, including a large chromosome, two minichromosomes, and 91 transposable IS elements; (2) the purple membrane regulon, which programs the accumulation of large quantities of the light-driven proton pump, bacteriorhodopsin, and allows for a period of phototrophic growth; (3) components of the sophisticated pathways for color-sensitive phototaxis; (4) the gas vesicle gene cluster, which codes for cell buoyancy organelles; (5) pathways for the production of carotenoid pigments and retinal, (6) processes for the repair of DNA damage; and (7) putative homologs of circadian rhythm regulators. We conclude with a discussion of the power of systems biology for comprehensive understanding of Halobacterium NRC-1 photobiology.

Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea

The minimal number of genes required for the formation of gas vesicles in halophilic archaea has been determined. Single genes of the 14 gvp genes present in the p-vac region on plasmid pHH1 of Halobacterium salinarum (p-gvpACNO and p-gvpDEFGHIJKLM) were deleted, and the remaining genes were tested for the formation of gas vesicles in Haloferax volcanii transformants. The deletion of six gvp genes (p-gvpCN, p-gvpDE, and p-gvpHI) still enabled the production of gas vesicles in H. volcanii. The gas vesicles formed in some of these gvp gene deletion transformants were altered in shape (Delta I, Delta C) or strength (Delta H) but still functioned as flotation devices. A minimal p-vac region (minvac) containing the eight remaining genes (gvpFGJKLM-gvpAO) was constructed and tested for gas vesicle formation in H. volcanii. The minvac transformants did not form gas vesicles; however, minvac/gvpJKLM double transformants contained gas vesicles seen as light refractile bodies by phase-contrast microscopy. Transcript analyses demonstrated that minvac transformants synthesized regular amounts of gvpA mRNA, but the transcripts derived from gvpFGJKLM were mainly short and encompassed only gvpFG(J), suggesting that the gvpJKLM genes were not sufficiently expressed. Since gvpAO and gvpFGJKLM are the only gvp genes present in minvac/JKLM transformants containing gas vesicles, these gvp genes represent the minimal set required for gas vesicle formation in halophilic archaea. Homologs of six of these gvp genes are found in Anabaena flos-aquae, and homologs of all eight minimal halobacterial gvp genes are present in Bacillus megaterium and in the genome of Streptomyces coelicolor.

Evaluation of oxygen permeability of gas vesicles from cyanobacterium Anabaena flos-aquae

The enhancement of oxygen permeability in aqueous medium by addition of cyanobacterial gas vesicles (GVs) has been examined. The GVs were isolated from cultures of Anabaena flos-aquae that had been cultivated in photobioreactors and harvested by dark flotation. Prior to the permeability experiments, the collected GVs were treated with glutaraldehyde for improved stability. Measurements of oxygen permeability were made with a polarographic oxygen electrode in suspensions of various GV volume fractions (0-2.1%). The experimental results were compared with the values predicted theoretically (Fricke's equation) assuming different permeability through the GVs (PmGV), ranging from 0 to 8.30 x 10(-4) mol m-1 atm-1 s-1. The former corresponded to impermeable vesicles, the latter to air at 22 degrees C as if there were no vesicle wall. The best-fit value of PmGV was 9.9 x 10(-7) mol m-1 atm-1 s-1, ca. 36-fold higher than that in water. GVs were therefore very permeable to oxygen. However, the value was much lower than that predicted for air, implying the existence of wall resistance.

Miniprep DNA isolation from unicellular and filamentous cyanobacteria

A rapid miniprep method for isolation of DNA from 12 strains of cyanobacteria belonging to groups I, III, IV and V is described. The protocol is a modification of the methods of Boyle and Lew [Boyle, J.S., Lew, A.M., 1995. An inexpensive alternative to glassmilk for DNA purification. Trends Genet. 11, 8] and the cetyltrimethyl ammonium bromide (CTAB) extraction method of Sahgai-Maroof et al. [Sahgai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., Allard, R.W., 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci. USA 81, 8014-80181. The new method is especially useful for obtaining cyanobacterial DNA from unicellular, filamentous and filamentous branched species. The method does not require phenol extraction and the product can be used directly for PCR amplification and restriction digestion.

Poles apart: biodiversity and biogeography of sea ice bacteria

This review introduces the subjects of bacterial biodiversity and biogeography. Studies of biogeography are important for understanding biodiversity, the occurrence of threatened species, and the ecological role of free-living and symbiotic prokaryotes. A set of postulates is proposed for biogeography as a guide to determining whether prokaryotes are "cosmopolitan" (found in more than one geographic location on Earth) or candidate endemic species. The term "geovar" is coined to define a geographical variety of prokaryote that is restricted to one area on Earth or one host species. This review discusses sea ice bacteriology as a test case for examining bacterial diversity and biogeography. Approximately 7% of Earth's surface is covered by sea ice, which is colonized principally by psychrophilic microorganisms. This extensive community of microorganisms, referred to as the sea ice microbial community (SIMCO), contains algae (mostly diatoms), protozoa, and bacteria. Recent investigations indicate that the sea ice bacteria fall into four major phylogenetic groups: the proteobacteria, the Cytophaga-Flavobacterium-Bacteroides (CFB) group, and the high and low mol percent gram-positive bacteria. Archaea associated with sea ice communities have also been reported. Several novel bacterial genera and species have been discovered, including Polaromonas, Polaribacter, Psychroflexus, Gelidibacter, and Octadecabacter; many others await study. Some of the gram-negative sea ice bacteria have among the lowest maximum temperatures for growth known, < 10 degrees C for some strains. The polar sea ice environment is an ideal habitat for studying microbial biogeography because of the dispersal issues involved. Dispersal between poles is problematic because of the long distances and the difficulty of transporting psychrophilic bacteria across the equator. Studies to date indicate that members of some genera occur at both poles; however, cosmopolitan species have not yet been discovered. Additional research on polar sea ice bacteria is needed to resolve this issue and extend our understanding of its microbial diversity.

Flotation characteristics of cyanobacterium Anabaena flos-aquae for gas vesicle production

Cyanobacterium Anabaena flos-aquae was cultivated in photobioreactors for production of intracellular gas vesicles (GVs), as potential oxygen microcarriers. Natural flotation of the buoyant culture was investigated as a potential means of cell harvesting, because filtration and centrifugation tended to destroy the vesicles. Best flotation was found with actively growing culture and when conducted in the dark. The flotation-related cell properties, including the specific GV content, vesicle-collapsed filament density, and intracellular carbohydrate content, were measured to understand the phenomena. During the batch culture, the specific GV content remained relatively constant at 370 microL/(g dry cells) but the filament density (ranging 1.02 to 1.08 g/cm3) showed a decrease-then-increase profile. The increase began when the growth slowed down because of the reduced light availability at high cell concentrations. The dark flotation was studied with both actively growing (mu approximately 0.2 day-1) and stationary-phase cultures. The specific GV content of the stationary-phase culture remained relatively constant while that of the growing culture increased slightly. The intracellular carbohydrate content of the growing culture decreased much faster and more significantly, from 57 to 10 mg/(g dry cells) in </= 8 h. The filament density also decreased, apparently parallel to the profiles of carbohydrate content.

Expression of the Kdp ATPase is consistent with regulation by turgor pressure

The kdpFABC operon of Escherichia coli encodes the four protein subunits of the Kdp K+ transport system. Kdp is expressed when growth is limited by the availability of K+. Expression of Kdp is dependent on the products of the adjacent kdpDE operon, which encodes a pair of two-component regulators. Studies with kdp-lac fusions led to the suggestion that change in turgor pressure acts as the signal to express Kdp (L. A. Laimins, D. B. Rhoads, and W. Epstein, Proc. Natl. Acad. Sci. USA 78:464-468, 1981). More recently, effects of compatible solutes, among others, have been interpreted as inconsistent with the turgor model (H. Asha and J. Gowrishankar, J. Bacteriol. 175:4528-4537, 1993). We re-examined the effects of compatible solutes and of medium pH on expression of Kdp in studies in which growth rate was also measured. In all cases, Kdp expression correlated with the K+ concentration when growth began to slow. Making the reasonable but currently untestable assumptions that the reduction in growth rate by K+ limitation is due to a reduction in turgor and that addition of betaine does not increase turgor, we concluded that all of the data on Kdp expression are consistent with control by turgor pressure.

Solar ultraviolet and the evolutionary history of cyanobacteria

On the basis of photobiological, evolutionary, paleontological, paleoenvironmental and physiological arguments, a time course for the role of solar ultraviolet radiation (UVR, wavelengths below 400 nm) in the ecology and evolution of cyanobacteria is proposed in which three main periods can be distinguished. An initial stage, before the advent of oxygenic photosynthesis, when high environmental fluxes of UVC (wavelengths below 280 nm) and UVB (280-320 nm) may have depressed the ability of protocyanobacteria to develop large populations or restricted them to UVR refuges. A second stage lasting between 500 and 1500 Ma (million years), started with the appearance of true oxygen-evolving cyanobacteria and the concomitant formation of oxygenated (micro)environments under an oxygen free-atmosphere. In this second stage, the age of UV, the overall importance of UVR must have increased substantially, since the incident fluxes of UVC and UVB remained virtually unchanged, but additionally the UVA portion of the spectrum (320-400 nm) suddenly became biologically injurious and extremely reactive oxygen species must have formed wherever oxygen and UVR spatially coincided. The last period began with the gradual oxygenation of the atmosphere and the formation of the stratospheric ozone shield. The physiological stress due to UVC all but disappeared and the effects of UVB were reduced to a large extent. Evidence in support of this dynamics is drawn from the phylogenetic distribution of biochemical UV-defense mechanisms among cyanobacteria and other microorganisms. The specific physical characteristics of UVR and oxygen exposure in planktonic, sedimentary and terrestrial habitats are used to explore the plausible impact of UVR in each of the periods on the ecological distribution of cyanobacteria.

Structural characteristics of halobacterial gas vesicles

Gas vesicle formation in halophilic archaea is encoded by a DNA region (the vac region) containing 14 different genes: gvpACNO and gvpDEFGHIJKLM. In Halobacterium salinarum PHH1 (which expresses the p-vac region from plasmid pHH1), gas vesicles are spindle shaped, whereas predominantly cylindrical gas vesicles are synthesized by the chromosomal c-vac region of H. salinarum PHH4 and the single chromosomal mc-vac region of Haloferax mediterranei. Homologous complementation of gvp gene clusters derived from the chromosomal c-vac region led to cylindrical gas vesicles in transformants and proved that the activity of the c-gvpA promoter depended on a gene product from the c-gvpE-M DNA region. Heterologous complementation experiments with transcription units of different vac regions demonstrated that the formation of chimeric gas vesicles was possible. Comparison of micrographs of wild-type and chimeric gas vesicles indicated that the shape was not exclusively determined by GvpA, the major structural protein of the gas vesicle wall. More likely, a dynamic equilibrium of several gvp gene products was responsible for determination of the shape. Transmission electron microscopy of frozen hydrated, wild-type gas vesicles showed moiré patterns due to the superposition of the front and back parts of the ribbed gas vesicle envelope. Comparison of projections of model helices with the moiré pattern seen on the cylindrical part of the gas vesicles provided evidence that the ribs formed a helix of low pitch and not a stack of hoops.

Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli

Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. In halobacteria, gas vesicle production is encoded in a 9-kb cluster of 14 genes (4 of known function). In cyanobacteria, the number of genes involved has not been determined. We now report the cloning and sequence analysis of an 8,142-bp cluster of 15 putative gas vesicle genes (gvp) from Bacillus megaterium VT1660 and their functional expression in Escherichia coli. Evidence includes homologies by sequence analysis to known gas vesicle genes, the buoyancy phenotype of E. coli strains that carry this gvp gene cluster, the presence of pressure-sensitive, refractile bodies in phase-contrast microscopy, structural details in phase-contrast microscopy, structural details in direct interference-contrast microscopy, and shape and size revealed by transmission electron microscopy. In B. megaterium, the gvp region carries a cluster of 15 putative genes arranged in one orientation; they are open reading frame 1 and gvpA, -P, -Q, -B, -R, -N, -F, -G, -L, -S, -K, -J, -T, and -U, of which the last 11 genes, in a 5.7-kb gene cluster, are the maximum required for gas vesicle synthesis and function in E. coli. To our knowledge, this is the first example of a functional gas vesicle gene cluster in nonaquatic bacteria and the first example of the interspecies transfer of genes resulting in the synthesis of a functional organelle.

Detection of toxin-producing cyanobacteria by use of paramagnetic beads for cell concentration and DNA purification

Early detection of water blooms caused by potential toxin-producing cyanobacteria is important in environmental monitoring. We present a new nucleic acid-based method for detection of cyanobacteria in water that utilizes the same paramagnetic solid phase (beads) for both bacterial cell concentration and subsequent DNA purification. In the cell concentration step, the beads were attracted to a magnet after cell adsorption (in an alcohol- and salt-containing solution), and the supernatant was removed. For DNA purification, a buffer containing guanidine thiocyanate and Sarkosyl lysed the concentrated cells. The addition of alcohol precipitated the released DNA onto the same solid phase as was used for the cell concentration. Finally, to remove PCR inhibitors, the DNA was washed twice in alcohol while bound to the beads. All of the bead-DNA complex was used in the subsequent PCR amplification. The detection limit, as measured by 16S rDNA PCR amplification, was 50 cells in a 0.5-ml water sample, which is considerably lower than the limit (500 cells/ml) of toxic cyanobacteria tolerated in drinking water (New South Wales Blue-Green Algae Task Force, 1992). Testing of water from natural habitats showed a detection limit in the same range as that for the defined samples. The detection limits and the simplicity of the method (paramagnetic beads can be handled in automated systems) suggest that our method is suitable for routine environmental monitoring.

Growth competition between Halobacterium salinarium strain PHH1 and mutants affected in gas vesicle synthesis

To investigate the role of the buoyancy provided by gas vesicles in the facultative anaerobe Halobacterium salinarium PHH1, the growth of a gas-vacuolate (Gv+) strain in competition with two gas-vesicle-defective (Gvdef) mutants was examined. The Gv+ strain synthesized gas vesicles throughout its growth cycle, and floated up to form a thick surface scum during the exponential growth phase in static culture. Mutant Gvdef1 produced significantly fewer gas vesicles than the Gv+ strain in corresponding stages of growth, although in late stationary phase a small proportion of cells floated up to the surface of static cultures. Mutant Gvdef2 had a much lower gas vesicle content in shaken culture and produced negligible amounts of gas vesicles in static culture. The Gv+ and the two Gvdef strains grew equally well in shaken cultures, but in static cultures, where steep vertical gradients of oxygen concentration were established, Gvdef1 was outgrown by the Gv+ strain. Gvdef2 outcompeted the Gv+ strain in shallow static cultures, perhaps because Gvdef2 carried a smaller protein burden, which offset the benefits of buoyancy. This selection for Gvdef2 was lost in deeper static cultures, although it could be restored by aerating static cultures from below. The results support the hypothesis that the role of buoyancy in halobacteria is to maintain cells at the more aerated surface of brine pools.

What size should a bacterium be? A question of scale

There are living prokaryotes (Bacteria and Archaea) that have cell sizes that range from 0.02-400 microns3. Over this tremendous range, various abilities to cope with the environment are needed. This review attempts to formulate some of the problems and some of the solutions. The smallest size for a free-living organism is suggested to be largely set by the catalytic efficiency of enzymes and protein synthetic machinery. Because of fluctuations in the environment, cells must maintain machinery to cope with various catastrophes; these mechanisms increase the minimum size of the cell. On the other hand, the largest cell is reasonably assumed to be limited by the ability of diffusion to bring nutrients to the appropriate part of the cell and to dispose of waste products. To explore the limitation imposed by diffusion, analysis is developed of diffusion processes through stirred and unstirred media, diffusion through media that contains obstacles, and the effect of size and shape.

Transcript analysis of the c-vac region and differential synthesis of the two regulatory gas vesicle proteins GvpD and GvpE in Halobacterium salinarium PHH4

Halobacterium salinarium PHH4 synthesizes gas vesicles in the stationary growth phase by the expression of 14 gyp genes arranged in two clusters. The chromosomal gvpACNO (c-gvpACNO) gene cluster (encoding the major structural gas vesicle protein GvpA and the minor structural protein GvpC was transcribed as three mRNA species starting at one promoter during the stationary phase of growth. The second gene cluster, c-gvpDEFGHIKLM), was transcribed during all stages of growth as a relatively unstable, single mRNA with a maximal length of 6 kb. In addition, a 1.7-kb c-gvpD transcript was synthesized during stationary growth starting at the same promotor as that of the cgvpDEFGHIJKLM mRNA. The expression of the first two genes located in this unit (c-gvpD and c-gvpE) was also monitored by Western blot (immunoblot) analyses using antisera raised against these proteins synthesized in Escherichia coli. While the cGvpD protein was present only during early exponential growth and disappeared during gas vesicle formation, the cGvpE protein was present during cGvpA and gas vesicle synthesis in the early stationary phase of growth. Previous data indicated that cGvpD is involved in repression of gas vesicle formation, whereas cGvpE is a transcriptional activator for the c-gvpA promoter. The appearance of both proteins during the growth cycle is in line with the functions of these proteins in gas vesicle synthesis. The mechanism of the differential translation of cGvpD and cGvpE from the c-gvpDEFGHIJKLM rnRNA still has to be elucidated, but antisense RNAs complementary to the 5' terminus as well as the 3' portion of the c-gvpD mRNA might be involved in this regulation. Such RNAs occurred during early stationary growth when the cGvpD protein level decreased and may possibly inhibit the translation of the c-gvpD mRNA.

Functional studies of the gvpACNO operon of Halobacterium salinarium reveal that the GvpC protein shapes gas vesicles

Gas vesicle (Vac) synthesis in Halobacterium salinarium PHH1 involves the expression of the plasmid pHH1-encoded vac (p-vac) region consisting of 14 different gvp genes that are arranged in two clusters, p-gvpACNO and, oriented in the direction opposite to that of gvpA, p-gvpDEFGHIJKLM. The p-gvpACNO region was analyzed at the transcriptional and functional levels in H. salinarium and in Haloferax volcanii transformants containing subfragments of the p-vac region. The p-gvpACNO genes were transcribed as several mRNAs: the 270-nucleotide (nt) p-gvpA transcript, encoding the major structural protein, occurred in large amounts, and minor amounts of three different readthrough transcripts (p-gvpACN, and p-gvpACNO mRNA) were found. In addition, the p-gvpO gene gave rise to two separate mRNA species: a 550-nt mRNA starting at the ATG and spanning the entire reading frame and a 420-nt RNA encompassing the second half of the p-gvpO gene. The requirement of p-gvpC, p-gvpN, and p-gvpO gene expression for gas vesicle synthesis was assessed by transformation experiments using the VAC- species Haloferax volcanii as the recipient. A delta C transformant, harboring the p-vac region with a deletion of the p-gvpC gene, produced large amounts of irregularly shaped gas vesicles. A shape-forming function of p-GvpC was demonstrated by complementation of the delta C transformant with the p-gvpC gene, resulting in wild-type-shaped gas vesicles. In the delta N transformant, the level of gas vesicle synthesis was very low, indicating that the p-GvpN protein is not required for gas vesicle assembly but may enhance gas vesicle synthesis. The p-gvpN deletion did not affect accumulation of p-gvpACO mRNA but reduced the separate p-gvpO transcription. The delta O transformant was Vac- and had a strongly decreased level of p-gvpACN mRNAs, demonstrating that the p-GvpO protein is required for gas vesicle synthesis and may affect transcription of this DNA region.

Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water

Psychrophilic, gas vacuolate, heterotrophic bacteria indigenous to sea ice communities in Antarctica have been isolated. Phylogenetic analysis of representative members of these bacteria shows that they belong to the alpha, beta, and gamma Proteobacteria and the Flavobacteria-Cytophaga group. This is the first report of gas vacuolate bacteria from the beta Proteobacteria and the Flavobacteria-Cytophaga groups.

The gvpA/C cluster of Anabaena flos-aquae has multiple copies of a gene encoding GvpA

Southern analysis of genomic DNA from Anabaena flos-aquae revealed that the genes encoding the two authenticated protein components of cyanobacterial gas vesicles, GvpA and GvpC, were carried on the same 4.9-kb HindIII restriction fragment. By comparing the hybridization intensities observed when either gvpA- or gvpC-specific oligonucleotides are bound to this HindIII fragment, we calculated that the A. flos-aquae genome contains seven copies of gvpA and a single copy of gvpC. The nucleotide sequence of the longest cloned section of the gvpA/C cluster of A. flos-aquae DNA revealed the presence of four complete copies of gvpA and part of a fifth copy located upstream from a single copy of gvpC; no clones carrying the entire gvpA/C-bearing HindIII fragment were identified. The distribution of Sau3A restriction sites throughout the gvpA/C-bearing genomic HindIII fragment resembled that seen in the cloned portion of the gvpA/C cluster and is consistent with that expected for a cluster containing seven copies of gvpA and one copy of gvpC. The length of transcripts that hybridize to both gvpA and gvpC on Northern blots was consistent with a 7gvpA + 1gvpC transcriptional unit.

Wild-type gas vesicle formation requires at least ten genes in the gvp gene cluster of Halobacterium halobium plasmid pNRC100

To study the functions of the 13 gvp genes, gvpMLKJIHGFEDACN, on plasmid pNRC100 of Halobacterium halobium in gas vesicle formation, we carried out linker scanning mutagenesis of the gene cluster. We constructed a 24.5-kb Escherichia coli-H. halobium shuttle plasmid, pFL2, containing the gvp gene cluster and introduced a kanamycin resistance (kappa) cassette into each gene (except for gvpA). Transformation of H. halobium SD109, which had the entire gvp gene cluster deleted, with pFL2 and mutated pFL2 derivatives showed that while the unmutated gene cluster successfully programmed gas vesicle formation, derivatives with insertion of the kappa cassette in any of the gvp genes, except gvpM, did not lead to production of normal gas vesicles. Insertions in gvpL, -K, -J, -I, and -F resulted in a complete block in gas vesicle synthesis, while insertions in gvpH, -G, -E, -D, -C, and -N resulted in greatly reduced gas vesicle synthesis. In most cases, the block in gas vesicle synthesis did not result from polar effects, since similar results were obtained for derivatives of the insertion mutants in which most of the internal portion of the kappa cassette was deleted and only small (15 to 54-bp) insertions remained. The only exceptions were for gvpH and gvpD, where deletion of the internal portion of the kappa insertions resulted in phenotypic reversion. Electron microscopic analysis of the kappa mutants revealed that interruptions of gvpC and gvpN result in the formation of smaller gas vesicle than in the wild type, while interruptions of gvpF, -G, -H, -J, -K, and -L produce no discernible vesicle intermediates. These results indicate the gvpA, -C, and -N, which have the rightward transcriptional orientation, encode structural proteins, with gvpC and gvpN necessary for late stages of vesicle formation, and gvpL, -K, -J, -I, -H, -G, and -F, which have the leftward transcriptional orientation encode proteins involved in early steps in the assembly of gas vesicles.