Modular drug design software?
5 hours ago in The Curious Wavefunction
"Our results show that quorum sensing is a social trait, susceptible to exploitation and invasion by cheats. Given this, how is quorum sensing maintained in natural populations?"This is rather sneaky. The authors have just nicely shown that, in mixed laboratory cultures optimized to make growth dependent on protease secretion, cells that use protease secreted by other cells are favoured. So it's probably legitimate to describe protease production under these conditions as a social trait. But they jump over the question of whether natural populations grow under comparable conditions. Instead they just allow us assume this, and go on to propose the explanation they want to test:
"The most likely explanation is kin selection - if neighbouring cells are close relatives they will have a shared interest in communicating honestly and cooperating."What? No mention of the by-far more likely explanation that autoinducers exist mainly for a cell-autonomous function (diffusion sensing) that is not subject to cheating? This is the first big problem with this paper.
The distributed genome hypothesis (DGH) states that pathogenic bacteria possess a supragenome that is much larger than the genome of any single bacterium, and that these pathogens utilize genetic recombination and a large, non-core set of genes as a means of diversity generation.Well, that's certainly very relevant to our analysis of the distribution of transformability! Now we just need to clarify, first for ourselves and then for potential readers of our manuscript, how having a diversity of competence and transformation phenotypes fits into this.
Unexpectedly, we have found that the expression of at least 165 genes is upregulated in the presence of ComK. These include open reading frames (ORFs) that were previously shown to be ComK dependent as well as many for which there was no prior evidence of ComK control. In several cases, validation of the microarray data was achieved through the use of promoter fusions. This profound alteration in the expression programme involves many genes that appear to have no role in transformation. We propose that competence as usually defined is but one feature of a differentiated, growth-arrested state, which we propose to call the K-state.And here are the last paragraphs from their Discussion:
It is certain that many (probably most) of the newly identified ComK-dependent genes are not required for competence, originally defined as receptivity to transformation (Lerman and Tolmach, 1957), nor for the recombination and recovery steps that follow DNA uptake. We have demonstrated that this is the case for pta and oxdC/yvrL, and it is certainly true for many of the 29 intermediary metabolism genes, the six sporulation genes and many of the newly identified ComK-dependent transcriptional regulators. It is therefore no longer appropriate to refer to the ComK-determined physiological state as 'competence', as more is involved than transformability. We propose to refer to this instead as the 'K-state', a neutral term with no functional connotation.Arresting DNA replication is a fairly desperate measure, and I'd like to know what makes the K-state worth the risk. Despite the statements above about competence being only one of the K-state's functions, Dubnau's group seems to have slipped back into assuming it's the only function. Here's a paragraph from the Discussion of a more recent paper on how the K-state is triggered and maintained or lost (Maamar & Dubnau 2005, 56:615-624). It assumes that competence is the function of the K-state and that transformation is the function of competence. It then constructs an evolutionary just-so story to explain why only small fractions of the cells in a lab culture enter this state:
The cell shape and cell division genes are of particular interest, as the K-state is associated with inhibition of cell elongation and division (Hahn et al., 1995; Haijema et al., 2001). The competence gene comGA plays a role in the inhibition of these two processes. One ComK-dependent gene cluster (Fig. 2) includes the genes for Maf (an inhibitor of cell division that has also been implicated in DNA repair; Butler et al., 1993; Minasov et al., 2000), MreB, MreC, MreD (shape determining factors; Jones et al., 2001), MinC and D (inhibitors of cell division; Levin et al., 1992) and RadC, a probable DNA repair protein. In addition to this cluster, mbl, tuaF, tuaG, cwlH and cwlJ are activated. Mbl plays a role in cell shape determination (Henriques et al., 1998; Jones et al., 2001), TuaG and F are required for the synthesis of teichuronic acid (Soldo et al., 1999), and CwlH and J are cell wall hydrolases. It appears that the K-state is accompanied by a reprogramming of cell shape, cell division and cell wall synthesis genes.
A minority of the cells in a given population reach the K-state, and these cells are arrested in cell division and growth (Haijema et al., 2001). The reversal of this growth inhibition requires at least the degradation of ComK (Turgay et al., 1998). In this sense, the K-state appears to be in some respects a resting state and is associated with the induction of a number of genes (exoA, radC, recA, ssb, topA, maf and dinB) that are likely to be involved in DNA repair. The arrest of cell division and growth may be an advantage if the K-state has evolved in part to deal with DNA damage, or if DNA repair is required after transformation, as growth in the presence of DNA lesions may be detrimental. In E. coli, the SulA protein is induced as part of the SOS regulon and inhibits cell division (Bi and Lutkenhaus, 1993), presumably until DNA damage has been repaired. Several genes that are activated in the K-state might facilitate the assimilation of novel nutritional sources. These include malL, sucD, yoxD and ycgS and the putative transport genes pbuX, yckA, yckB, ycbN, ywfF, yvrO, yvrN, yvrM, yqiX, ywoG and yvrP. Several of these transport proteins, in particular ywfF and ywoG, might function instead as detoxifying efflux pumps. In this connection, it is worth mentioning some additional ComK-dependent genes. oxdC encodes an acid-induced oxalate dehydrogenase (Tanner and Bornemann, 2000), which has been suggested to play a role in pH homeostasis in response to acid stress. hxlA and hxlB encode enzymes of the ribulose monophosphate pathway (Yasueda et al., 1999), and hxlR encodes a positive activator of their expression. It was suggested that this pathway is involved in the detoxification of formaldehyde. ComK induces all three of these genes. Additional stress response genes that are apparently upregulated in response to ComK include groES and possibly yqxD. Finally, two genes are likely to be involved in the synthesis of antibiotics (sboA and cypC; Hosono and Suzuki, 1983; Matsunaga et al., 1999), which may serve to eliminate competitors.
In conclusion, we propose that the K-state is a global adaptation to stress, distinct from sporulation, which enables the cell to repair DNA damage, to acquire new fitness-enhancing genes by transformation, to use novel substrates (possibly including DNA; Redfield, 1993; Finkel and Kolter, 2001) and to detoxify environmental poisons. This view of the K-state suggests a reason for its expression in only a fraction of the cells in a given population. The K-state represents a specialized strategy for dealing with danger, but also carries with it inherent risks. Transient arrest of growth and cell division confer vulnerability to overgrowth by competing populations, and transformability opens the cell to invasion by foreign DNA. The genome may therefore activate alternative systems in subpopulations to deal with adversity, and the K-state may be one such system. This strategy maximizes the probability that the genome will survive when faced with changing environments, a valuable capability for a soil-dwelling organism.
It has been known for many years (Nester and Stocker, 1963; Hadden and Nester, 1968; Haseltine-Cahn and Fox, 1968) that competence in the domesticated laboratory strains of B. subtilis, is expressed in 10–20% of the cells in a given culture (Fig. 2B). In natural isolates of B. subtilis, the fraction of cells expressing competence is markedly lower than this, presumably because these strains have not been artificially selected for high transformability. In one such isolate, only about 1% of the cells express a comK–gfp fusion, but in these rare cells, expression is at a high level (J. Hahn, H. Maamar and D. Dubnau, unpubl.) This dramatic example of population heterogeneity may have evolved so that few cells in a clone will commit to a particular fitness-enhancing strategy. As the prolonged semidormancy that accompanies the K-state (Haijema et al., 2001) poses a potential challenge to survival, this strategy serves to minimize risks to the genotype. If, on the other hand, the few cells expressing the K-state happen to enjoy an advantage, the chances that the genotype will survive will be enhanced. Presumably the heterogeneity mechanism has evolved to maximize the benefit-to-risk ratio. There may be many examples of population heterogeneity selected by evolution in single celled organisms (see for instance Balaban et al., 2004), and an understanding of the mechanisms that regulate this heterogeneity would be of general interest.