Genome watch: Bacterial minimalism
2
more than 3.7 Mb, compared with another parasite Nanoarchaeum equitans, the genome of which is 0.49 Mb 2 . The B. bacteriovorus genome is arranged as a single circular mole- cule that encodes 3,584 coding sequences (CDS). B. bacteriovorus is a member of the δ-proteobacteria, which is a morphologically diverse class that also includes sulphate- reducing or sulphur-reducing dissimilatory bacteria and myxococci. It is essentially ubiqui- tous in the environment where it targets other Gram-negative bacteria as prey. The authors’ well-constructed account of the B. bacteriovorus genome project links the findings from the genome to the eight phases of its predatory life cycle 1 . In stage I, B. bacteri- ovorus takes the form of a fast-moving motile ‘swimmer cell’ and the genome revealed six clusters of motility and flagella biosynthesis genes, in addition to multiple flagellin- encoding genes, which makes this bacterium an ‘all-terrain vehicle’ that is presumably adapted for differing liquid viscosities. In stage II of the life cycle, once B. bacteriovorus has come into contact with its prey, an impressive array of different pili are synthe- sized — the genome reveals the fourth largest repertoire of pil genes reported for any bacte- rial genome sequenced so far and includes both multiple pil genes organized into four clusters and individual pil genes. The authors speculate that a set of twitching-type pili could have a role in the entry process, possibly by pulling the bacterium through a small pore in the outer membrane and peptidoglycan layer of the prey and into the periplasm. After entering the periplasm, the flagella are shed (stage III) and DNA replication begins (stage IV). Incredibly, the entry pore in the host cell is resealed after bdellovibrio entry. Once inside, B. bacteriovorus tightly coordi- nates the expression of multiple hydrolytic enzymes that are used for bioconversion of the host, including peptidases/proteases (150), glycanases (10), DNases (20), RNases (9) and lipases (15). An equally large set (245) of membrane-transport proteins is also expressed, presumably to recover the break- down products of the hydrolytic enzymes. At this stage, the host cell, although retaining integrity, loses its original shape and forms cells with a characteristically rounded morphotype, known as bdelloplasts (stage V). HIGHLIGHTS 274 | APRIL 2004 | VOLUME 2 www.nature.com/reviews/micro Minimalism in microbiology could be interpreted as a reduction in cell size or a reduction in genome content. Three genomes this month illustrate both of these interpretations. Bdellovibrios are small cells, perhaps because the bdellovibrio life cycle involves entering into, and feeding inside, a host bacterium, which is often as small as 1 µm in diameter. However, even small bdellovibrio cells have a relatively large genome of 3.7 Mb, which is presumably necessary to encode the information that is required for their complicated life cycle. By contrast, mycoplasmas and phytoplasmas, which also reside inside a host cell, have a reduced minimal genome content. Examples of mycoplasma and phytoplasma sequences have recently been published, which could provide further insights into the minimal information requirements for microbial life. The recent publication of the Bdellovibrio bacteriovorus genome sequence 1 represented a new frontier for genome sequencing by expanding the breadth of our knowledge from bacterial pathogens that cause disease in higher plants, animals and humans, to bacterial pathogens that prey on bacteria. B. bacteriovorus is small — 0.2–0.5-µm wide and 0.5–2.5-µm long — but has a surprisingly large genome, of B. bacteriovorus remains in the periplasm and it is not known whether substrates, such as nucleotides from the host cytosol, are trans- ported across the cytoplasmic membrane using host-transport systems, or whether B. bacteriovorus uses its own transport systems — the authors favour the latter hypothesis. B. bacteriovorus can either use the biomole- cules of the prey directly, or degrade them and re-synthesize its own metabolites. Indeed, there is evidence, which indicates that both methods are used — for example, the lack of amino acid biosynthetic pathways indicates that host-derived amino acids are essential for protein synthesis. Conversely, the panoply of hydrolytic enzymes indicates that catabolism of the host is equally important. Still within the bdelloplast, B. bacteriovorus cells undergo filamentation, develop septa (stage VI) and form flagellated daughter cells (stage VII), which are released into the envi- ronment after crossing the host cell outer membrane for the second time (stage VIII). One surprising finding is the lack of evidence for recent horizontal gene transfer in B. bacte- riovorus — with the exception of a new pro- phage sequence. This is despite its predatory life cycle, which involves consorting with and consuming other bacteria. The fascinating biology and the genome sequence of B. bacteriovorus will undoubtedly intensify interest in this organism. Its potential use as a ‘living antibiotic’ will also push it into the political limelight in future debates about the use of genetically modified organisms (GMO). Mycoplasma mycoides subsp. mycoides biotype small colony type (MmymySC) 3 is the aetiological agent of contagious bovine pleu- ropneumonia (CBPP) in cattle (FIG. 2), which is a highly contagious respiratory disease with serious socio-economic consequences. It is the only bacterial disease, together with Bacterial minimalism Mohammed Sebaihia, Nicholas Thomson, Lisa Crossman and Julian Parkhill GENOME WATCH Figure 1 | Bdellovibrio bacteriovorus infecting prey. B. bacteriovorus is shown in yellow, the bacterial prey cell is shown in blue. Image courtesy of Stephan C. Schuster, Snjezana Rendulic and Jürgen Berger (Max–Planck Institute for Developmental Biology, Tübingen, Germany). One surprising finding is the lack of evidence for recent horizontal gene transfer in B. bacteriovorus
Transcript of Genome watch: Bacterial minimalism
more than 3.7 Mb, compared with anotherparasite Nanoarchaeum equitans, the genomeof which is 0.49 Mb2. The B. bacteriovorusgenome is arranged as a single circular mole-cule that encodes 3,584 coding sequences(CDS). B. bacteriovorus is a member of the δ-proteobacteria, which is a morphologicallydiverse class that also includes sulphate-reducing or sulphur-reducing dissimilatorybacteria and myxococci. It is essentially ubiqui-tous in the environment where it targets otherGram-negative bacteria as prey.
The authors’ well-constructed account ofthe B. bacteriovorus genome project links thefindings from the genome to the eight phases ofits predatory life cycle1. In stage I, B. bacteri-ovorus takes the form of a fast-moving motile‘swimmer cell’ and the genome revealed sixclusters of motility and flagella biosynthesisgenes, in addition to multiple flagellin-encoding genes, which makes this bacteriuman ‘all-terrain vehicle’ that is presumablyadapted for differing liquid viscosities. Instage II of the life cycle, once B. bacteriovorushas come into contact with its prey, animpressive array of different pili are synthe-sized — the genome reveals the fourth largestrepertoire of pil genes reported for any bacte-rial genome sequenced so far and includesboth multiple pil genes organized into fourclusters and individual pil genes. The authorsspeculate that a set of twitching-type pilicould have a role in the entry process, possiblyby pulling the bacterium through a small porein the outer membrane and peptidoglycanlayer of the prey and into the periplasm. Afterentering the periplasm, the flagella are shed(stage III) and DNA replication begins (stageIV). Incredibly, the entry pore in the host cellis resealed after bdellovibrio entry.
Once inside, B. bacteriovorus tightly coordi-nates the expression of multiple hydrolyticenzymes that are used for bioconversion ofthe host, including peptidases/proteases(150), glycanases (10), DNases (20), RNases(9) and lipases (15). An equally large set (245)of membrane-transport proteins is alsoexpressed, presumably to recover the break-down products of the hydrolytic enzymes. Atthis stage, the host cell, although retainingintegrity, loses its original shape and formscells with a characteristically roundedmorphotype, known as bdelloplasts (stage V).
H I G H L I G H T S
274 | APRIL 2004 | VOLUME 2 www.nature.com/reviews/micro
Minimalism in microbiology could beinterpreted as a reduction in cell size or areduction in genome content. Threegenomes this month illustrate both of theseinterpretations. Bdellovibrios are small cells,perhaps because the bdellovibrio life cycleinvolves entering into, and feeding inside, ahost bacterium, which is often as small as 1 µm in diameter. However, even smallbdellovibrio cells have a relatively largegenome of 3.7 Mb, which is presumablynecessary to encode the information that isrequired for their complicated life cycle. By contrast, mycoplasmas andphytoplasmas, which also reside inside ahost cell, have a reduced minimal genomecontent. Examples of mycoplasma andphytoplasma sequences have recently beenpublished, which could provide furtherinsights into the minimal informationrequirements for microbial life.
The recent publication of the Bdellovibrio bacteriovorus genome sequence1 represented a new frontier for genome sequencing byexpanding the breadth of our knowledge frombacterial pathogens that cause disease in higherplants, animals and humans, to bacterialpathogens that prey on bacteria. B. bacteriovorusis small — 0.2–0.5-µm wide and 0.5–2.5-µmlong — but has a surprisingly large genome, of
B. bacteriovorus remains in the periplasmand it is not known whether substrates, suchas nucleotides from the host cytosol, are trans-ported across the cytoplasmic membraneusing host-transport systems, or whether B. bacteriovorus uses its own transport systems— the authors favour the latter hypothesis.B. bacteriovorus can either use the biomole-cules of the prey directly, or degrade themand re-synthesize its own metabolites. Indeed,there is evidence, which indicates that bothmethods are used — for example, the lack ofamino acid biosynthetic pathways indicatesthat host-derived amino acids are essential forprotein synthesis. Conversely, the panoply ofhydrolytic enzymes indicates that catabolism of the host is equally important.
Still within the bdelloplast, B. bacteriovoruscells undergo filamentation, develop septa(stage VI) and form flagellated daughter cells(stage VII), which are released into the envi-ronment after crossing the host cell outermembrane for the second time (stage VIII).One surprising finding is the lack of evidencefor recent horizontal gene transfer in B. bacte-riovorus — with the exception of a new pro-phage sequence. This is despite its predatorylife cycle, which involves consorting with andconsuming other bacteria.
The fascinating biology and the genomesequence of B. bacteriovorus will undoubtedlyintensify interest in this organism. Its potentialuse as a ‘living antibiotic’ will also push it intothe political limelight in future debates aboutthe use of genetically modified organisms(GMO).
Mycoplasma mycoides subsp. mycoidesbiotype small colony type (MmymySC)3 is theaetiological agent of contagious bovine pleu-ropneumonia (CBPP) in cattle (FIG. 2), whichis a highly contagious respiratory disease with serious socio-economic consequences.It is the only bacterial disease, together with
Bacterial minimalismMohammed Sebaihia, Nicholas Thomson, Lisa Crossman and Julian Parkhill
GENOME WATCH
Figure 1 | Bdellovibrio bacteriovorus infectingprey. B. bacteriovorus is shown in yellow, thebacterial prey cell is shown in blue. Image courtesyof Stephan C. Schuster, Snjezana Rendulic andJürgen Berger (Max–Planck Institute forDevelopmental Biology, Tübingen, Germany).
One surprising finding isthe lack of evidence forrecent horizontal genetransfer in B. bacteriovorus
H I G H L I G H T S
NATURE REVIEWS | MICROBIOLOGY VOLUME 2 | APRIL 2004 | 275
14 viral diseases, that is included in the A-listof the World Organization for Animal Health(see the online links box) — which lists trans-missible diseases that have the potential forserious and rapid spread, that are of seriouseconomic or public health consequence and that are important in the internationalanimal trade.
MmymySC belongs to the Class Mollicutes— the smallest free-living cell-wall-less bacte-ria — which are thought to have evolved froman ancestral Gram-positive bacterium with alow G+C content through a process of reduc-tive evolution. The genome of MmymySCstrain PG1T (1.21 Mb) is the seventh myco-plasma genome to be sequenced, after thepublication of four human mycoplasmapathogens (Mycoplasma genitalium, Myco-plasma pneumoniae, Mycoplasma penetransand Ureaplasma urealyticum), one murinemycoplasma pathogen (Mycoplasma pulmo-nis) and one avian mycoplasma pathogen(Mycoplasma gallisepticum). At 24%, theG+C content of the MmymySC genome isthe lowest among the bacterial genomes thathave been sequenced so far. The 985 pre-dicted CDS include 72 that form part ofinsertion sequences (IS) and encode trans-posases. IS elements constitute 13% of the
MmymySC genome, which is the most IS-dense bacterial genome that has beensequenced so far. The presence of multiple ISelements might be responsible for the anom-alies in the G+C skew of the MmymySCgenome. Despite the availability of six othermycoplasma genomes, 27% of MmymySCCDS are unique and have no assigned function,which highlights the lack of understanding ofeven these minimalist organisms.
The basis for the severity of the diseasecaused by MmymySC is largely unknown.However, the genome sequence provides cluesto the mechanism of pathogenesis. MmymySChas a redundant complement of capsulebiosynthesis genes, which could increase itsvirulence and help in avoidance of the hostimmune system. Antigenic variation,through mutation in homopolymeric repeatsin the promoters or coding regions of surfaceproteins, is another mechanism that somemycoplasmas use to evade the host immunesystem. As well as a previously identifiedphase-variable lipoprotein gene, two otherlipoprotein genes that underwent high-frequency phase variation during the shotgunstage of the sequencing project were detectedin the MmymySC genome sequence. Further-more, there are 14 additional candidate phase-variable genes — three that encode lipoproteinsand 11 that encode surface proteins. The pro-duction of active oxygen-containing moleculesis also likely to have a role in virulence. Thisstems from an earlier observation that the lessvirulent European MmymySC strains producereduced amounts of hydrogen peroxide com-pared with the more virulent African andAustralian strains. Although the geographicalorigin of the sequenced strain is unknown,two clusters of genes that are involved in theproduction of hydrogen peroxide have beenidentified in the genome. Interestingly, some ofthese genes are either truncated or missing inthe European strains.
Similar to the mycoplasmas, phytoplasmashave no cell walls and reside inside the phloem(nutrient-carrying vessels) of plants. They aretransmitted between host plants by insectleafhopper vectors, and the sequenced straincauses the economically important diseaseOnion Yellows (FIG. 3). Previously sequencedobligate plant pathogens reside in the xylem(water-carrying vessels) of plants. For theshotgun sequencing approach of phyto-plasma strain OY (Candidatus Phytoplasmaasteris)4, chromosomal DNA was extracteddirectly from infected garland chrysan-themums. The P. asteris OY genome is just860 kb and possesses fewer metabolic genesthan do many mycoplasmas. So, it is an idealorganism to study for those interested in the
minimal set of genes that are necessary forlife. Oddly, there seem to be multiple, redun-dant copies of the genes uvrB, hflB, tmk, damand ssb, which are normally present as a singlecopy in bacteria. The most surprising findingwas the absence of ATP synthase, which indi-cates that ATP might be imported from thehost by an unknown mechanism. There isevidence to indicate that phytoplasmasimport multiple host-cell metabolites forgrowth, which could perturb host cellularmetabolic functions, thereby leading to dis-ease. The presence of several transporter pro-teins in the genome seems to substantiate thishypothesis.
Mohammed Sebaihia, Nicholas Thomson,Lisa Crossman and Julian Parkhill are at the SangerInstitute, Wellcome Trust Genome Campus, Hinxton,Cambridge CB10 1SA, UK.e-mail: [email protected]:10.1038/nrmicro869
1. Rendulic, S. et al. A predator unmasked: life cycle ofBdellovibrio bacteriovorus from a genomic perspective.Science 303, 689–692 (2004).
2. Waters, E. et al. The genome of Nanoarchaeum equitans:insights into early archaeal evolution and derived parasitism.Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003).
3. Westberg, J. et al. The genome sequence of Mycoplasmamycoides subsp. mycoides SC type strain PG1T, thecausative agent of contagious bovine pleuropneumonia(CBPP). Genome Res. 14, 221–227 (2004).
4. Oshima, K. et al. Reductive evolution suggested from thecomplete genome sequence of a plant-pathogenicphytoplasma. Nature Genetics 36, 27–29 (2004).
Online links
DATABASESThe following terms in this article are linked online to:Entrez: http://www.ncbi.nlm.nih.gov/Entrez/Bdellovibrio bacteriovorus | Candidatus Phytoplasma asteris |Mycoplasma mycoides subsp. mycoides small colony type |Nanoarchaeum equitans
FURTHER INFORMATIONWellcome Trust Sanger Institute:http://www.sanger.ac.ukWorld Organization for Animal Health:http://www.oie.int/eng/en_index.htmAccess to this interactive links box is free online.
Figure 3 | Candidatus Phytoplasma asterisinfecting plant phloem. A section of phloem tissuefrom an infected plant vascular bundle is shown.Several of the plant cells contain Phytoplasma cells.Image courtesy of Shigetou Namba (The Universityof Tokyo, Japan).
Figure 2 | Mycoplasma mycoides subsp.mycoides biotype small colony type disease.A diseased cow lung is shown, with necrotic tissueowing to MmymySC infection. Image photographedby John Bashiruddin, courtesy of Anja Persson andMathias Uhlén (Royal Institute of Technology (KTH),Stockholm, Sweden).
The P. asteris OY genome isjust 860 kb and possessesfewer metabolic genes thando many mycoplasmas.
