On Shape

by Manuel Sánchez Angulo

This articles is reprinted in translation from the exceptional blog Curiosidades de la Microbiología, cour­te­sy of the blogmaster, Manuel Sánchez. We thank him most sincerely for giving us his permission.

 

(Click to enlarge )
Figure 1. Myriad morphologies have evolved throughout the bacterial domain. This phylogenic tree includes 26 kinds of shapes. The abbreviations refer to the main taxa. Colors indicate the various types of shapes. See the ex­ten­ded legend below for more information. The bacteria are not shown to scale. Source

If there is one thing that draws attention to the study of eukaryotes, it is the enormous diversity of their mor­pho­lo­gy, from the largest sequoias to the smallest radiolaria. Prokaryotes, on the other hand, seem rather simple and boring. If you open page 109 of the 7^th edition of Mur­ray, Rosenthal, and Phaller's "Medical Microbiology" you will find that there are only four cell types: cocci, bacilli, cur­ved bacilli, and spirochetes. In fact, that's because bac­te­ri­o­lo­gy has traditionally been a medical discipline, and those are the typical morphological types of pathogenic bacteria. What also helped to firm up the idea that the bacteria are either bacilli or cocci is that the model micro­or­ga­nisms of molecular biology are Escherichia coli, Ba­cil­lus subtilis and Streptococcus pneumoniae. When one ob­serves bacteria in the environment, however, the di­ver­sity of sizes and shapes found has nothing to be­grudge that of other living beings.
 

This is precisely what is described in the article "Diversity Takes Shape: Understanding the Me­cha­nis­tic and Adaptive Basis of Bacterial Morphology" by Kysela, Randich, Caccamo, and Brun. The authors not only offer a catalog of the various bacterial forms, but they also discuss their im­por­tance in evolution. Recall that in biology one of the most important paradigms is that of struc­ture-function. Thus, the morphology of a living being has probably helped it survive in the habitat it oc­cupies. The shape of bacteria has been shaped by natural selection, so understanding how that di­versity may have come about can give us insights into how bacteria work.
 

(Click to enlarge )
Figure 2. Peptidoglycan syn­the­sis ma­chinery in E. coli. Elongation is carried out by the elongasome and division by the di­vi­so­me. In both cases, a cytoplasmic scaffold is needed to direct the localization of pep­ti­do­gly­can (orange) synthesis and to recruit va­ri­ous components, such as membrane elements that include regulatory proteins, precursor-syn­the­sizing proteins (blue), and peptidoglycan mo­di­fi­ers (red). Of all these proteins, the most con­ser­ved in all bac­te­ri­al groups are FtsZ (orange) and FtsK (blue). Source

Bacterial morphology was initially used as an important taxonomic criterion. Any bacteria with distinguishing characteristics, such as having a spiral form, possessing prosthecae (distinct cellular appendages), being pho­to­tro­phic and helical, grouped in clusters, etc., were lump­ed together in higher or lower taxa. However, with the arrival of molecular phylogeny, many of those taxa had to be "restructured." In the article, the authors give the example of the Betaproteobacteria Rhodocyclus tenuis and Rubrivivax gelatinosus that previously were included within the genus Rhodospirillum in class Al­pha­pro­teo­bac­te­ria. This is as if spiders had been erroneously been classified as insects.
 

Combining metagenomic and morphological data results in a phylogenetic tree that illustrates how the shape of bacteria in different phyla has evolved (see Fig. 1). Sha­pes such as helical (green) or filamentous (red) ap­pear scattered throughout the tree. This indicates that this type of shape arose independently and repeatedly in evolution. In such a case where two different lineages come to have the same morphology, is that form ge­ne­ra­ted by a convergent molecular strategy? Or is it because the species have similar lifestyles?
 

In other instances, a given morphology becomes grouped in a region of the tree, for example, the branches of the Ac­tinobacteria (purple) or the appendages of the Cau­lo­bac­teria (blue). Here, the morphology has been inherited from a common ancestor to all that group­ing. The questions then are somewhat dif­ferent: is the persistence of this form due to se­lec­tive pressure? If not all members of that group are equal, how and why can morphological variations arise?
 
 
 
 

Figure 3. Incorporation of peptidoglycan into mor­phologically distinct bacteria. A shows elon­gation, B division. In both E. coli and B. subtilis, the elongation zones are arranged along a spi­ral. When the cells are to divide, the zonal syn­the­sis localizes only in the center of the bac­te­ri­um. In S. pneumoniae, elongation occurs when new material is inserted into a so-called equa­to­ri­al ring. As new material is inserted, the re­sult­ing rings separate, indicating the future place of septation. In S. aureus there is no elongation, only septal peptidoglycan synthesis. Source

What is clear is that we don't know why some bacteria have a certain shape and not another. In general, mor­pho­logical features can be attributed to adaptation to selective forces as diverse as nutrient acquisition, sur­face adhesion, dispersion, predator evasion, or co­lo­ni­za­tion of a host. If we look at the shapes that appear in the phy­lo­ge­ne­tic tree, some are easy to associate with a cer­tain lifestyle. For example, he­lical shapes are op­ti­mal for swim­­ming in viscous liquids; large filaments usu­ally are an ad­aptation to avoid being swallowed by pro­tists; bran­ching in an aquatic bacterium modifies its buo­yancy, al­lowing it to control depth and thus to be placed in a nu­trient-rich zone of the water column. Some shapes even serve to fulfill more than one func­tion. Her­petosiphon is a bac­te­ri­um that forms long fi­la­ments that intersect each other. This prevents it from being devour­ed by protozoa, but it also allows it to create a network with "holes" where hy­dro­ly­tic enzyme secretions serve to lyse other bacteria, on which it feeds.
 

But how do bacteria acquire their shape?

The truth is that we know rather little, since what is known is based on the study of a few bacteria: the cocci Streptococcus pneumoniae or Staphylococcus aureus; the rod-shaped Escherichia coli or Bacillus subtilis, and the curved/spiral-shaped Helicobacter pylori, Caulobacter crescentus, or Bor­re­lia burgdorferi. Not much is known about the rest of bacterial shapes. So perhaps we should re­think the question and figure out if there is a simpler one that we can answer. For example:
 

What aspect of morphogenesis do all bacteria have in common?

• All have peptidoglycan walls (except for mycoplasmas, thermoplasmas, and perhaps a few others) and their shape, at the molecular level, is determined by this macromolecule. So it is not surprising that the biochemical machinery responsible for the synthesis of the wall has been preserved among the various bacterial phyla. At the molecular level, this enzymatic equip­ment is localized in a certain "zone" of the bacterium, which is where it exerts its function. This could be called "zonal synthesis"
• The wall synthesis machinery must not only ensure that shape is maintained and the size of the bacterium increases due to elongation, it must also allow cell reproduction by sep­ta­tion. Changing the orientation of peptidoglycan synthesis permits transition from elongation to septum formation. But it is necessary that both processes remain coordinated in space and time to ensure the survival of the bacteria.
   

Figure 4. Zonal synthesis of peptidoglycan and bac­terial morphology. In the prosthecate Al­pha­pro­te­o­bac­te­ria, the peptidoglycan syn­thesis ma­chinery (green) is suffi­cient for dif­ferent pro­sthe­ca position phenotypes to ap­pear. A C. cres­cen­tus, polar prostheca. B Asticcacaulis ex­cen­tri­cus, subpolar prostheca. C Asticcacaulis bi­­pro­­sthe­­cum, bipolar prosthecae. D the branched phe­no­type of the actinobacteria Streptomyces coe­licolor. Source

We could say that these are the "ground rules" that all bac­teria have to follow. Perhaps each bacterial group has some specific rules that explain morphological dif­fer­en­ces. Or perhaps, one might expect that if two bacteria have a bacillary form it will be because they both follow the same set of rules. The best example is Escherichia coli (Gram negative) and Bacillus subtilis (Gram positive). Both elongate thanks to placement of their en­zy­ma­tic equipment in areas that follow a spiral pat­tern, and thus synthesize the new peptidoglycan following this path.
 

The fact that two phylogenetically distinct bacteria have solved the problem in the same way points to the 'so­lu­tion' having appeared long ago. But when we ob­serve in detail what happens in other taxonomic groups (see Fig. 3), what at first sight seems to be an evo­lu­tio­na­ry con­ser­va­tion is actually an evo­lu­tio­na­ry convergence. Within each species we find a myriad of shapes. Ob­serv­ing an evolutionary convergence tells us something else: if the zonal synthesis machinery is re­po­si­tion­ed, a great diversity of bacterial forms can be generated, all of them derived from the rod-sha­ped morphology. For example, if the zonal synthesis is re­stric­ted to only one of the poles, we can obtain a prostheca such as in C. crescentus. In contrast, if the zonal synthesis is distributed along the length of a filament, we get the branching observed in the Actinobacteria. The various bac­te­ri­al shapes result from using the same basic rules, just differently.
 

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Figure 5. Phylogenetic tree of the Caulobacterales (A) and their cellular mor­pho­lo­gy (B). 1 Bilateral prostheca, A. bi­pro­sthe­cum (C. Jiang, Stanford Uni­versity). 2 subpo­lar pro­sthe­ca, A. excentricus (C. Jiang, Stanford Uni­versi­ty). 3 polar prostheca, C. crescentus (P. Cac­camo, In­diana University). 4 polar prostheca, Ma­ricaulis maris (P. Viollier, University of Ge­ne­va). 5 small polar prostheca, Brevundimonas subvibriodes (B. Heckel, Indiana University). 6 Polar pro­sthe­ca for budding, Hirschia baltica. Source

Combining single-cell genomics with high-resolution mi­cro­sco­py, the research group of Yves Brun has been able to study the evolution of the prostheca among species of Cau­lo­bac­te­ra­les. The phylogenetic tree below shows that the polar prostheca (present in C. crescentus) appeared first. In some species this prostheca has become a zone spe­ci­a­li­zed for budding (Hirschia baltica), but in others this zone has been lost and the bacterium has returned to a rod shape (C. segnis). In other species, the zonal syn­the­sis was repositioned in a subpolar region (As­tic­ca­cau­lis excentricus), and from this group it was re-positioned to a bilateral position, thus increasing the number of pro­sthe­cae (A. biprosthecum). Upon closer examination of this transition, the researchers found a protein called SpmX that is responsible for coordinating the synthesis of peptidoglycan in the prosthecae. This protein has a domain that varies in each of these species, and directs the location of the zonal synthesis.
 

Could the great diversity of bacterial shapes be explained by zonal synthesis of peptidoglycan ? In­deed, it is quite li­kely that the combination of genomic methods and new microscopic imaging technologies will allow novel experimental approaches to answer this ques­tion. Such studies may tell us why bac­te­ria look the way they do. They may even address the prob­lem of re­la­ting bacterial shape to the forces of se­lec­tion that act on it. One could certainly say that this field of research is taking shape.
 

 

 

 

 

Extended legend to Fig. 1. Black dots denote ancestral nodes of selected major taxa: DT Deinococcus-Thermus; Ac Ac­ti­no­bac­te­ria; Cf Chloroflexi; Cn Cyanobacteria; Fi Firmicutes (inclusive of Mollicutes); Sp Spirochetes; PVC Planctomycetes, Ver­rucomicrobia, Chlamydiae; Cb Chlorobi; Bd Bacteroidetes; α, β, γ, δ, ε, Proteobacteria subdivisions. 1 Bifidobacterium lon­gum. 2 Streptomyces coelicolor (mycelial [=multicellular] filament with hyphae and spores). 3 Corynebacterium diphtheriae (two cells, dumbbell and club shapes). 4 Herpetosiphon aurantiacus (filament of multiple cylindrical cells). 5 Calothrix (fi­la­ment of multiple disk-shaped cells). 6 Mycoplasma genitalium. 7 Spiroplasma culicicola. 8 Lactococcus lactis (predivisional cell). 9 Borrelia burgdorferi. 10 Gimesia maris (previously Planctomyces maris, predivisional cell with proteinaceous stalk). 11 Prosthecochloris aestuarii. 12 Pelodictyon phaeoclathratiforme (filament of multiple trapezoidal cells). 13 Spirosoma linguale. 14 Muricauda ruestringensis (appendage includes nonreproductive bulb). 15 Desulfovibrio vulgaris (two cells, he­li­cal and curved shapes). 16 Helicobacter pylori. 17 Caulobacter crescentus (predivisional cell). 18 Hyphomonas neptunium (predivisional cell). 19 Rhodomicrobium vannielii (filament of multiple ovoid cells, one is predivisional). 20 Pro­sthe­co­mi­cro­bi­um hirschii. 21 Simonsiella muelleri (filament of multiple curved cells). 22 Nevskia ramosa (two cells with bifurcating slime stalk). 23 Beggiatoa leptomitiformis (filament of multiple, giant cylindrical cells). 24 Thiomargarita nelsonii (single giant cell). 25 Escherichia coli. 26 Mariprofundus ferrooxydans (single cell with metal-encrusted stalk). Bacterial schematics are not to scale. Species names are colored according to morphology as indicated in the key. Colored dots are appended to indicate species with multiple morphologies. Names of species depicted in schematics are emphasized in large, bold font.