Moselio Schaechter

  • The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet. I will emphasize the unusual and the unexpected phenomena for which I have a special fascination... (more)

    For the memoirs of my first 21 years of life, click here.

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March 17, 2014

The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective.

by Suckjoon Jun

I entered the bacterial chromosome field in 2004 as a fresh Ph.D. trained in theoretical physics. Ten years is not long enough for one to gain the depth and breadth of a scientific discipline of long history, certainly not for an early career scientist to write an essay of the status of A Mathematician’s Apology (Hardy 1940). Nevertheless, I agreed to write this Perspective as a physicist who entered biology, because my colleagues are often curious to know what drives physicists to become (physical) biologists, and make them stay in biology despite many challenges. I also wanted to share several lessons I have learned because, while some of them are personal and specific to my field, I have a good reason to believe that they might resonate with many future travelers. This Perspective is for them.

I would like to start with the story of one of the most familiar and yet mysterious forces in nature—gravity. Galileo is said to have dropped two balls of different masses from leaning Tower of Pisa in Italy some five hundred years ago. His experiment was to demonstrate that, on the contrary to Aristotle’s theory, the falling rate of the balls was independent of their mass. A modern version of this experiment was performed on the Moon by the Commander of Apollo 15 with a hammer and a feather. For a movie of this experience, click here. When released from the same height at the same time, the two falling bodies hit the surface of the Moon simultaneously! On the Earth, however, the feather would have fluttered, as if alive, because of the air.

Initially attracted to the beauty of Amsterdam, I started my post-doctoral research at AMOLF, an interdisciplinary research institute known for exciting interactions at the interface between physical and biological sciences. The forces I was interested in were much less tangible than gravity. In particular, I was supposed to explain the driving force underlying segregation of a replicating chromosome in Escherichia coli. It sounded simple to me, except that I barely knew anything about bacteria, certainly without realizing that it was one of the long-standing problems in biology. I knew the DNA biophysics literature fairly well, but when I saw the beautiful 1992 illustration of E. coli in Goodsell, it was obvious that something like the wormlike chain model was not going to be very useful to understand segregation of the whole chromosome. What worried me was the directionality—if I were a small protein sitting on a replicating chromosome, could I tell which DNA segment belongs to which sister DNA? Physicists like questions like that, whether they are rooted in physics or biology.

Continue reading "The Bacterial Chromosome: A Physical Biologist's Apology. A Perspective." »

July 29, 2013

The Planctomycetes, Tricky Gram-negatives Awaiting Genetic Manipulation

by Marco Allemann

Figure 1. The original interpretation of the G. obscuriglobus cellular organization. Thin section of cryosubstituted bud cell with large nuclear body bounded by a “nuclear envelope” (E) consisting of two membranes between which is a clear electron-transparent space. The nuclear body contains ribosome-like particles as well as a nucleoid. It is surrounded by cytoplasm that contains superficially similar ribosome-like particles and is bounded by a single intracytoplasmic membrane (ICM). Bar: 200 nm. Source.

Members of the bacterial phylum Planctomycetes (click here and here) inhabit a wide variety of environments throughout the world. What makes them special is that in the mind of some investigators they possess a mix of eukaryotic and prokaryotic structural attributes. Now that is something pretty unique and worth contemplating. This group of organisms has been previously described in this blog by previous graduate students. So this serves as an update, which is timely because there is critical news on the plancto front.

What Do You See Inside The Planctos?

Under the electron microscope, sectioned Planctomycetes cells reveal that their internal membrane is highly folded into apparent compartment, including a purported membrane-bound nuclear region. It has been suggested that this arrangement, almost unheard of among prokaryotes, is evidence for the planctos being a “missing link” between Bacteria and Eukaryotes. The linchpin for this notion that the planctos may be some kind of remnant of eukaryogenesis has been their “nuclear envelope,” which is thought to totally surround the nucleoid. There are yet other arguments in favor of this notion, e. g., they are able to endocytose and they divide by budding (although so do other bacteria, such as Caulobacter crescentus). In addition, those planctos capable of anammox (anaerobic ammonia oxidation coupled with nitrate reduction) contain an organelle, a membrane-bound structure called the anammoxosome. Yet, the presence of organelles is not unique to this group of bacteria. Of interest is also that planctos do not contain peptidoglycan in their cell wall, something limited to few bacteria. Surprisingly, they carry genes encoding for known outer membrane proteins and peptidoglycan synthesis, although in this regard they may not be all that unique either because chlamydiae and mycoplasmas also lack peptidoglycan, plus the chlamydiae also carry genes for its synthesis.

Continue reading "The Planctomycetes, Tricky Gram-negatives Awaiting Genetic Manipulation" »

June 06, 2013

Pictures Considered #5. The Birth of the FtsZ Ring

by Elio

Thin section of an E. coli cell in the process of dividing showing gold-labeled anti-FtsZ-antibody particles located at the septum.

The first cytoskeletal protein discovered in bacteria was FtsZ, the tubulin-like maker of the contractile ring involved in cell division of most bacteria. It was found by investigating one of a series of Fts (for “Filamenting temperature sensitive”) conditional mutants, first constructed by Y. Hirota, A. Ryter and F. Jacob in the 1960’s. These mutants do not divide but grew as filaments at a non-permissive temperature. Joe Lutkenhaus became acquainted with such mutants in the late 1970’s while a postdoc in Willie Donachie’s lab in Edinburgh. On his own, he continued studying such mutants and ended up purifying the FtsZ protein. Once he had it on hand, he made antibodies to it and, in an inspired moment, decided to look at the cellular localization of FtsZ using gold-labeled antibodies. What he found was of historic importance: although the antibody–carrying particles were distributed randomly in sections of most of the cells, in those cells that had initiated their septum and were engaged in cell division, the gold particles were located in a ring-shaped structure at the division septum. What this means was clearly stated in the paper: “….. we propose that FtsZ self-assembles into a ring structure on the cytoplasmic surface of the inner membrane where septation will occur and that is the first step in the division process. We also suggest that the initiation of FtsZ into a ring structure is the rate-limiting step for septation and occurs when the amount of FtsZ is sufficient.” One picture is all it took.

May 23, 2013

A Whiff of Taxonomy – The Phylum Elusimicrobia

by Elio

If you happen to look, you’ll find that new bacterial phyla spring up with amazing frequency, and that taxonomic names and facts accumulate at a staggering rate. As a public service, we’ll try from time to time to nibble away at this huge salami, slicing off and serving up one unfamiliar phylum at a time. Today it’s the turn of the Elusimicrobia. I admit that I chose them on account of their name. What could be more enticing than an elusive living being? (BTW, the name is derived from the Latin elusus, escaped from capture.)

An unrooted maximum-likelihood tree of 280 bacterial genomes, including the two sequenced representatives of the phylum Elusimicrobia, representing the regions of the bacterial domain currently mapped by genome sequences. Source.

This phylum used to be referred to as Termite Group 1, a monophyletic group of bacteria found as endosymbionts of flagellates in the hindguts of termites and other insects. Actually, Elusimicrobia are far less constrained than that, inhabiting also the ocean, soils, and sewage sludge. Since they form a deep branch of the bacterial tree, they are thought of as being quite old. The first one to be cultivated was given the apt name Elusimicrobium minutum. It is minute, an “ultramicrobacterium” only 0.17- 0.3 μm wide and variable in length. For an organism that can be grown in the lab, its genome is a puny 1.64 Mbp. It is a strict anaerobe but can grow on a variety of organic substrates. No pili have been seen on its surface although it is equipped with many of the genes needed for constructing pili. It presents the typical Gram-negative two-membrane system at its surface, but, perhaps due to its extreme thinness, it displays an interesting partitioning of its nucleoid (see the electron micrograph).

Continue reading "A Whiff of Taxonomy – The Phylum Elusimicrobia" »

May 20, 2013

Tit-for-Tat: A Bacterial Counterattack System

by Spencer Scott & John De Friel

Schematic diagram of a type VI secretion system by Y. M. Cully, C. Cambillau, and E. Cascales. The lower bilayer membrane is the attacker’s, the upper one the host’s. Notice the complex structure of the Type VI secretory apparatus. Source.

Microbial ecology may be a young field but it is well understood already that there is a broad spectrum of interactions between bacterial species, ranging from cooperative to competitive. In a recent paper researchers from John Mekalanos’ lab further characterized a recently discovered mechanism for inter-cell communication. This system, called the Type VI secretion system (T6SS), is a multi-protein complex native to many bacterial strains and structurally and functionally similar to a bacteriophage tail. The T6SS system is unique in that it is used as a weapon for injecting toxic proteins into the cytoplasm not only of animal host cells but also of neighboring bacterial cells by propelling its components through the neighbors’ membrane. The toxic effector proteins, Tse1 and Tse3, are peptidoglycan-degrading enzymes that can cause cell lysis in the absence of antitoxin proteins. For reviews, click here and here.

The Type VI Secretion System Differs in Two Species

To elucidate how and when a cell decides to inject a neighboring cell with its T6SS, these workers studied its behavior in Vibrio cholerae and Pseudomonas aeruginosa. In V. cholerae, the T6SS seems to shoot off at random, constantly showing up in different areas on the cell, which endows it with high pathogenicity and with the ability to kill off many other species of cells. In this light, V. cholerae can be seen as a sort of Yosemite Sam, a character renowned for his excessive and poorly aimed shooting. The analogy to this character and to Batman (see below) was thought up by Robert Cooper and appeared in his fine blog at Science 2.0.

Continue reading "Tit-for-Tat: A Bacterial Counterattack System" »

March 04, 2013

A PomZ Scheme For Turning One Cell Into Two

By William Margolin

Fig 1 Profzi Scheme
A pyramid scheme applied to academia. Source.

The division of one cell into two daughter cells is the crux of biological reproduction. But how do cells determine where along their dimensions division will occur? For bacteria, the best-studied species for basic biology, including cytokinesis, are the old standbys Escherichia coli, Bacillus subtilis, and Caulobacter crescentus, mainly because of their easy cultivation and genetic tractability. 

But, given bacterial diversity, the lifestyles of these representative workhorses aren’t necessarily the norm; they can even be relatively boring compared with the habits of others like the myxobacteria. One such species with exceptional behaviors is Myxococcus xanthus, whose cells travel in packs, eat other bacteria, and differentiate into fruiting bodies when their food runs out, eventually forming spores. Of course, in addition to moving around and eating a lot, myxobacterial cells still need to divide. Recent results from Lotte Søgaard-Andersen’s group and their collaborators show that the way myxobacterial cells select where to split into two is also out of the ordinary. 

Continue reading "A PomZ Scheme For Turning One Cell Into Two" »

February 11, 2013

The Gram Stain: Its Persistence and Its Quirks

by Elio

What is more emblematic of our science than the Gram stain? Since its invention 130 years ago, it has been in frequent and continuous use. It conveniently places most bacteria into one of two groups, the Gram-positives or the Gram-negatives. Gram staining is cheap, effective, quick, and relatively easy to interpret. Its most useful application is in the clinical setting. When examining a smear of, say, pus from an abscess, this stain often allows to include for consideration roughly half the clinically relevant bacterial species while excluding the others. Or consider a patient with meningitis. Here, speed is of the essence because treatment must be initiated right away. A Gram stain of the spinal fluid may reveal within minutes the presence of Gram-positive cocci, (probably pneumococci), Gram-negative cocci (almost certainly meningococci), or Gram-negative slender rods (most likely Haemophilus influenzae). This can make a critical difference in the choice of antibiotics that have to be administered in great haste. However, when it comes to characterizing the bacteria in an environment, its usefulness diminishes, in part because it is not always in step with taxonomy, which I’ll discuss below. And there yet is another side to this story. Quite a few bacterial species that stain positive early in the growth of a culture become Gram-negative later on. Does this detract from the value of Gram’s method? It may, but not in the hands of a person experienced in its use.

Continue reading "The Gram Stain: Its Persistence and Its Quirks" »

December 13, 2012

A Whiff of Taxonomy – Verrucomicrobia, The Bacterial Warthogs

by Elio

"We occasionally post very brief taxonomic pieces on selected bacterial groups. Be warned that we may not be fully attentive to the taxon level and may mix up genera and higher taxa."

A Verrucomicrobium. Source.

Unlike warthogs, likely to be considered beautiful only by their mother, the Verrucomicrobia  (verruca means “wart, thus the warty bacteria; more about this later) have considerable appeal, be it morphological, physiological, or ecological. This is yet another phylum that owes its recognition to nucleic acid technology. Although few of its members have been cultivated, 16S rRNA studies have confirmed that they are widely distributed in many environments, such as fresh water, oceans, soils, and even vertebrate feces.  Some are host-associated, their hosts including humans and, just because you need to know it, their proportion in the gut of ground squirrels increases as they hibernate. There are no known pathogens in this group although suspicion has arisen.  

Continue reading "A Whiff of Taxonomy – Verrucomicrobia, The Bacterial Warthogs" »

November 15, 2012

A Bacterium Learns Long Division

by Nanne Nanninga

The common picture of a dividing rod-shaped bacterium encompasses the positioning of the divisome, including an FtsZ-ring, in the cell center. This occurs after the cell has doubled its length without increasing its diameter. Conversely, increase in diameter without cell elongation would seem highly unlikely in a rod-shaped organism. Yet, this happens.

Figure 1: SEM of tightly apposed ectosymbionts on the surface of L. oneistus. Electron micrograph by N. Leisch.

In fact, this is the normal condition for an ectosymbiotic bacterium that lines the surface of the marine nematode Laxus oneistus. The symbiont is a g-proteobacterium like E. coli, but unlike E. coli it has not been cultured outside its natural habitat. As originally described by Polz et al. in the early nineties, the bacteria are positioned perpendicular to the surface of L. oneistus. They are glued to the surface of the nematode by a C-type lectin. The original paper already indicated that division takes place longitudinally, with one of the daughters presumed to remain attached to the nematode. This makes sense because otherwise the daughter cells would get lost to the environment. Recall that this phenomenon lies at the basis of the Helmstetter-Cooper baby machine, whereby one of a pair of newborn cells is selected to start a synchronous culture (Helmstetter et al.)

Recently, Leisch and colleagues have extended these observations by carefully determining cellular dimensions and visualizing the FtsZ division protein with fluorescent E. coli monoclonal antibodies. The results can be compared with E. coli data (Figure 2A, B). Whereas E. coli elongates as expected, this is not what happens with the symbiont. The symbiont does not change its length (Figure 2A) but increases its diameter (Figure 2B). Consequently, the symbiont divides longitudinally, (Fig. 2 C-H). Immunostaining of FtsZ reveals that FtsZ positioning correlates with the cell constriction. In fact, an ellipsoidal FtsZ-ring is observed stretched along the length of the endosymbiont.

Continue reading "A Bacterium Learns Long Division" »

October 08, 2012

Faster than a Speeding Bolt: Mycoplasma Walk This Way

(With a nod to Aerosmith)

by Daniel P. Haeusser

Many prokaryotes move actively in liquid (swim) or on moist solid surfaces (swarm and glide) toward or away from a stimulus, such as a nutrient, light, or oxygen. Not surprisingly, prokaryotes have evolved numerous means of locomotion built around distinct molecular mechanisms.

The motility of all animals, such as a human like Usain Bolt (A) or a goldfish (B) is based on the actin and myosin protein machinery. Many bacteria utilize completely different systems to achieve motility, such as the flagella in E. coli (C) or the unique ‘walking’ of M. mobile (D). These different motility systems are akin to various ways to make similar-looking boats move through the water, such as by the sails in Winslow Homer’s Breezing Up (A Fair Wind) (E) or the internal-combustion engine of the Batboat (F).

How distinct? A human running, a dog walking, an eagle flying, a fish swimming, a frog hopping, and a starfish crawling are each unique, but all share a root mechanism in the molecular properties of actin and myosin in muscle cells. For prokaryotes however, their movements don’t just look different; they often evolved from disparate molecular systems or organelles unique to a particular genus or even species . Some of the more-studied mechanisms of prokaryotic motility are flagellar-based swimming and swarming, type-IV pilus twitching motility, and the ‘adventurous’ motility of Myxococcus xanthus. This adventurous motility relies on both secreted polysaccharide and a helical motor that produces tread-like protrusions along the cell surface.

Among the handful of other known prokaryotic motility mechanisms are those employed by the Mycoplasma, a genus in the class Mollicutes of the low G+C Gram-positive bacteria (Firmicutes). (Video of Mycoplasma motility) The Mollicutes share several defining characteristics, most obviously the lack of cell wall that gives them their name (mollis is Latin for ‘soft’ or ‘pliable’). Therefore, although they phylogenetically fall in the Firmicutes, the Mollicutes have no cell wall for the Gram stain and are not susceptible to the antibiotics that target bacterial cell wall synthesis. In addition, the Mollicutes are some of the smallest cells known at 0.2 – 0.3 μm in length. Although they can be grown independently, these bacteria are often closely associated with host organisms, allowing the bacteria to attain drastically reduced genome sizes (The ~500,000 kilobases of M. genitalium is the lower limit for forming colonies on agar).

Continue reading "Faster than a Speeding Bolt: Mycoplasma Walk This Way" »

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