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a b c
Figure 1 | Biofilm formation and architecture. a, Individual bacteria b, These mushroom-like structures are characteristic of many submerged
undergo a reversible lifestyle switch between a nomadic and a sedentary biofilms. In this Pseudomonas aeruginosa biofilm, which was grown
existence. In the process, they lose motility and become enclosed in a gooey in a flow cell, they are about 150 m high. c, A biofilm of P. aeruginosa
extracellular matrix. As the community grows, different cell types appear grown on a semi-solid agar surface (about 10 mm in diameter). The
as the original strain diversifies to allow cells to take on different tasks colony displays aerial projections or wrinkling characteristic of an
or to exist in different ‘microniches’, shown by differently coloured cells. air-exposed biofilm.
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NATURE|Vol 441|18 May 2006 NEWS & VIEWS FEATURE
experimental reproducibility is best obtained are carried out respectively by proteins that
using single-species systems. As a consequence, Sedentary have structural domains possessing diguany-
(biofilm)
many microbial species have been analysed late cyclase and phosphodiesterase enzymatic
as monocultures. Yet, in natural settings, these activities (referred to as GGDEF and EAL
microbes nearly always grow in the context of Sensor domains, respectively, because of the highly
multi-species communities. To approximate the GGDEF conserved amino-acid sequences they con-
natural setting more closely, investigators have 2 GTP
tain). Genomic analyses of dozens of microbial
begun to foray into systems containing two or 2 GMP c-di-GMP genomes show that most bacteria harbour a
more microbial species. Some potentially inter- pGpG multitude of these proteins — Vibrio vulnifi-
esting multi-species model systems are poised cus, an extreme example, has 66 GGDEF
for molecular analyses. Among these are EAL proteins and 33 EAL proteins18. Often, the
mixed-species biofilms of the opportunistic Sensor GGDEF or EAL segment is fused to one
pathogens Pseudomonas aeruginosa (a bac- of several types of environment-sensing
terium) and Candida albicans (a fungus)4; two domains, implying that the production and
bacterial species that colonize teeth, Strepto- Nomadic breakdown of c-di-GMP are controlled by the
(planktonic)
coccus gordonii and Veillonella atypica5; and two bacterium’s surroundings.
species that occur in the soil environment Figure 2 | The lifestyle switch. The second- The GGDEF and EAL proteins, and by
around plant roots, P. aeruginosa and Agro- messenger molecule c-di-GMP mediates the extension c-di-GMP, are involved in many
bacterium tumefaciens6. switch between nomadic and sedentary lifestyles. diverse cellular activities, but the mechanism
Many species of bacteria have a multitude of by which c-di-GMP acts remains largely
Sticking together enzymes capable of making c-di-GMP from GTP unknown. It may act to integrate the many
Given the diversity of species that form (GGDEF proteins), and of breaking it down by external inputs sensed by GGDEF and EAL
biofilms, it is not surprising that the molecular hydrolysing it into GMP (EAL proteins). Overall, proteins, allowing this single messenger to
mechanisms involved in biofilm development it seems that increased intracellular levels of instigate multiple indirect effects. Or perhaps
c-di-GMP favour a sedentary existence, whereas
reflect the remarkable variety of the microbial there are small cellular ‘compartments’ where
reduced levels of the second messenger favour
world. Different species build biofilms differ- a nomadic existence. local fluctuations in the concentration of
ently, and many strains have multiple biofilm- c-di-GMP cause independent outcomes.
formation pathways. For instance, some that production of flagella and of extracellular Initially, c-di-GMP was shown to function by
mutants of the soil bacterium Pseudomonas matrix are mutually exclusive processes: bac- activating the enzyme that synthesizes extra-
fluorescens that cannot make a biofilm when teria give up the ability to move in order to set- cellular cellulose in Gluconoacetobacter xyli-
grown with glucose as the sole carbon source tle down. The regulatory circuitry involved in nus. This activity occurs at what is known as
do form biofilms when the sole carbon source this lifestyle switch is beginning to be mapped the post-translational level, once the target
is glutamate7. out. In Bacillus subtilis, for instance, the switch protein, in this case the enzyme, has been
So, do any general principles emerge? One between flagellar synthesis and matrix pro- synthesized19. By extension, investigators
feature that does seem to be common to all duction is controlled by the master gene regu- believed c-di-GMP acted exclusively at the
biofilms is that the cells secrete a ‘matrix’ to lator SinR (refs 13–15). This protein directly post-translational level on enzymes in other
hold themselves in place and to provide a represses genes encoding matrix components bacteria. But it now seems that c-di-GMP can
buffer against the environment. The make-up and activates those encoding flagellar compo- affect many processes, not only by acting
of each matrix is different, and, depending on nents (seemingly indirectly). SinR activity post-translationally, but also by regulating
the contributing species and environmental itself is antagonized by another protein, SinI, gene expression. For example, it functions at
conditions, there can be various mixes of poly- whose abundance and activity are modulated the level of gene-transcription control in
saccharides, proteins and even nucleic acids8. by changing environmental conditions. The P. aeruginosa20. No gene-regulatory proteins
The rich diversity among the matrix compo- inverse regulation of genes involved in motil- that bind to c-di-GMP have yet been identi-
nents can be glimpsed by mentioning what is ity and matrix components is apparent in fied conclusively, so how this messenger
known about the polysaccharides secreted by several other organisms, including E. coli, passes on the external signal to the master
just one species, P. aeruginosa, one of the most- P. aeruginosa, Salmonella enterica and Vibrio regulators is unclear.
studied organisms in terms of biofilm forma- cholerae, although the specific regulatory mol- Even though the structure of c-di-GMP and
tion. Many strains of this bacterium have the ecules used have not been identified16,17. its involvement in regulating cellulose synthe-
capacity to extrude at least three types of extra- But how is the lifestyle switch thrown? An sis in G. xylinus were reported21 in 1987, it was
cellular polysaccharide, called alginate, Pel and individual cell must have some way of recog- only in the past few years, when it became
Psl. Alginate was initially considered the major nizing that it is near a suitable surface, and of apparent that c-di-GMP occurs in bacterial
biofilm polysaccharide, but it now seems that passing that information on to the master pathogens, that interest in this molecule really
it is a major matrix component only of the gene regulators and other effectors so that intensified. In this sense, the history of
biofilms formed by unusual variants9. Pel and it can cease roaming and settle down. In sev- c-di-GMP research resembles the history of
Psl are apparently more ubiquitous: the genes eral species, the messenger seems to be a quorum sensing — the means by which bacte-
involved in the synthesis of Pel occur in all P. small cytoplasmic molecule called bis- ria detect the presence of others of their kind.
aeruginosa strains studied, whereas the genes (3–5)-cyclic dimeric guanosine monophos- As early as 1968, there were reports of what we
associated with Psl are present in only some10–12. phate (c-di-GMP)18 (Fig. 2). Low intracellu- now know as quorum sensing in the marine
But even the Pel genes have diverse regulatory lar c-di-GMP concentrations are found in bacterium Vibrio fischeri22. But it was only in
regions, suggesting that the various strains planktonic cells, but these levels rise once the the mid-1990s that quorum sensing was rec-
express this matrix component differently. cells have given up their nomadic lifestyle. ognized as a feature of many pathogens23, lead-
Furthermore, it looks as though c-di-GMP ing to a flood of interest in this process. One
Lifestyle choices can control the synthesis of diverse cellular has to wonder how many interesting molecu-
Motile bacteria generally have flagella — components involved in both motility and lar mechanisms have already been found in
corkscrew-like appendages that rotate to pro- matrix production in response to changing microbes but have yet to receive much atten-
pel them. These structures occur only in the environments. tion because they are not being studied in
microbes’ planktonic form, and it now seems The synthesis and degradation of c-di-GMP pathogens.
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NEWS & VIEWS FEATURE NATURE|Vol 441|18 May 2006
Box 1 Biofilms in human health and disease decade have the tools of molecular biology
been brought to bear on biofilms — a form
that has immense biological significance. With
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©2006 Nature Publishing Group