Small Things Considered

Talmudic Question #76

Do you think that our species is exempt from "kill-the-winner" predator-prey dynamics? (KTW is the colloquial term for the cyclical dynamic by which phages promote community evenness by reducing the numbers of the most abundant bacterial strains.)

Some Like It Curved

by Elio

Think about it: understanding what goes on inside any cell is hard enough. Add to that the complexities of being rod-shaped, and the mind starts to boggle. People have wondered about this aplenty. For sure, many expeditions  have set out to explore the poles of rod-shaped bacilli—how they are created, what molecules prefer to reside at this site and how this influences the physiology of the cell. In truth, definitive answers are generally wanting, but recent papers help us understand some of the complexities of rod-ness. A most readable review of the whole issue of polar localization is this one by Bardy and Maddock.

E. coli Cell Envelope Operating Instructions. (a) Proteins distributed
in the inner membrane are found in distinct domains e. g., polar, lateral,
and septal. Along the cylinder, some proteins are found at specific
locations, perhaps by associating with future cell division sites, or
because of the MreB helical filament. The membrane composition
varies, with CL significantly enriched at the cell poles (yellow shading).
(b) The peptidoglycan layer is inert at the poles (darker shading).
MreB-dependent and FtsZ-dependent insertion of new PG occurs
along lateral edge and septum, respectively (green diamonds). (c)
Polar outer membrane proteins are relatively immobile, as indicated by
the darker shading. (d) Composite overlay of images (a–c). Source.

A respectable number of reports describe the selective localization of proteins and lipids at or near bacterial poles and the septa. (See recent reviews by Kirkpatrick and Viollier and Shapiro, McAdams and Losick.) Proteins located at the poles include chemotaxis receptors (the first to be so localized), proteins involved in polar chromosome attachment, constituents of the cell division apparatus and their proteases, and many more. And, of course, there are such things as polar flagella, pili, and mechanosensitive channels. Overproduced proteins form aggregates (inclusion bodies) that end up at or near the poles, but that’s another story. Peptidoglycan also has a polar wrinkle in that the layer located at the poles differs from the rest in being metabolically inert; that is, it does not undergo turnover like that in the cylindrical part of the cell. So, bacteria are not just bags of enzymes. But how many times have you heard that?

Preaching to a Prokaryotic Choir

by Mark Martin

At my small liberal arts undergraduate institution, there is only one microbiology course, and it is generally taken by seniors. Here is an image of my Spring 2011 students, and below is the logo that the talented artist Kaitlin Reiss came up for our class T-shirts. One of my frustrations as an educator is how much I would like to tell students about microbiology, and how little time exists in my one course; if it were up to me, there would be a great deal more microbiology in freshman and sophomore biology courses. There is a reason that my students often call me a “microbial supremacist,” I suppose. Guilty as charged!

A Clever Bug That Is Difficile to Control

by S. Marvin Friedman

New infectious diseases emerge with worrisome frequency. Some accompany natural events such as changes in climate, while others surface with human help. Of great importance among the latter are the infections caused by Clostridium difficile (casually called C. diff). The prevalence of these infections is related to the use of certain gut-cleaning antibiotics such as clindamycin. In the pre-antibiotic era, C. diff infections were unknown, although they probably occurred once in a while.

A teichoic acid from Micrococcaceae. Source.

C. diff is a Gram-positive sporeformer that is now the foremost cause of nosocomial diarrhea worldwide. It can also cause more serious, life-threatening diseases, such as pseudomembranous colitis and, in elderly patients, a condition called toxic megacolon. The organism produces two powerful toxins that disrupt the host cell cytoskeleton. Usually this organism takes root in the intestines when the competing normal microbiota has been disrupted by antibiotic therapy. The classic homes for C. diff are hospitals and nursing home environments where ingestion of airborne, highly resistant spores is the usual source of infection. Relapses of C. diff infection (CDI) occur in about 20% of cases and can occur multiple times. Not only is the incidence of CDI on the rise (a 35-fold increase in the UK over the last decade), but there has been a concomitant increase in the severity of the disease, reflecting the emergence of highly virulent strains. This is not surprising, as C. diff displays a high degree of genomic fluidity (detailed here and here). On the other hand, hospitals are now doing a better job of controlling C. diff infection by paying more attention to hygiene (washing hands and bleaching surfaces in rooms where patients have been housed), by segregating C. diff patients, and, in some places, by instituting strict guidelines for antibiotic use. In recent years there has also been a sharp increase in C. diff infections in otherwise healthy individuals who are neither hospitalized nor taking antibiotics, thus attesting to this bug’s high degree of virulence and contagiousness.

Of Terms in Biology: Riboswitch

by Merry

Three known mechanisms of riboswitch action
after ligand binding. Red indicates the segment
of the riboswitch mRNA that undergoes a
conformational change upon binding of the
ligand. Ligand binding leads to: (a) formation
of a rho-independent transcription terminator
hairpin loop that terminates transcription; (b)
sequestration of the Shine-Dalgarno sequence
thus blocking translation initiation; (c) self-
cleavage by the mRNA. Source.

Recently we featured the term aptamer, and noted how useful these compounds are for researchers. We were talking of synthetic aptamers. But natural ones, in the form of RNA molecules, are part of an elegant mechanism that regulates gene expression in response to changing cellular levels of specific metabolites. These talented RNAs are known as riboswitches.

To be more precise, riboswitch is the name given to the domains in some mRNAs that bind directly to specific small molecular weight compounds and thus regulate expression of the genes encoded by that same mRNA. Riboswitches are generally located within the 5'-untranslated region of bacterial mRNAs. We need to define two more terms here, as a riboswitch is composed of two parts, also referred to as domains. One is a natural aptamer that possesses high specificity for a ligand and that adopts a different structure when bound to that ligand. Among Bacteria, these aptamer domains are typically 70-170 nucleotides long. The second domain is referred to as the expression platform as its job is to control expression of the adjacent ORF. How do they do it? The two domains overlap and influence each other. Binding of the ligand by the aptamer changes the conformation of the adjacent expression platform, which in turn represses expression of the ORF by interfering with either transcription or translation by a variety of mechanisms. Simple it isn’t.