An archaeum originally misclassified as bacterium: Sulfolobus acidocaldarius

The microbe Sulfolobus acidocaldarius was isolated from a hot spring in Yellowstone National Park in 1972 and originally misclassified as bacterium [1,2]. Thomas D. Brook and his team described the new genus Sulfolobus as sulfur-oxidizing bacteria with generally spherical cells producing frequent lobes—hence the term Sulfolobus. The isolated microbes were further characterized as acidophilic, living at an optimal pH of 2-3 and optimal temperatures of 70-75 °C—hence the epithet acidocaldarius. Microbes thriving at such temperatures are called hyperthermophiles.

About five years later the archaea domain was proposed by Carl Woese and George Fox. Following detailed genome studies, S. acidocaldarius was then taxonomically classified as belonging to the phylum or kingdom  crenarchaeota in the domain archaea. S. acidocaldarius serves now as a model organism for the Crenarchaeota and is used for many studies in archaeal biology [3,4].

Keywords: microbiology, hyperthermophile, crenarchaeon, nomenclature, taxonomy, history.

References and more to explore
[1] T. D. Brook, K. M. Brock, R. T. Belly and R. L. Weiss:  Sulfolobus: A new genus of sulfur-oxidizing bacteria living at pH and high temperature. Archives of Microbiology 1972, 84 (1), pp. 54-68. DOI: 10.1007/BF00408082.
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pages 110 and 111.
[3]  Microbe Wiki: Sulfolobus acidocaldarius [microbewiki.kenyon.edu/index.php/Sulfolobus_acidocaldarius].
[4] L. Chen et al.: The genome Sulfolobus acidocaldarius, a model organism of the Crenarcheota. Journal of Bacteriology 2005, 187 (14), pp. 4992-4999 [www.ncbi.nlm.nih.gov/pubmed/15995215].

Riding the fire sphere: Nanoarchaeum equitans

Nanoarchaeum equitans is one of the smallest living organisms known so far: a nano-sized (about 400 nm in diameter) microbe of the third domain,  named archaea [1-4]. The epithet equitans relates to the Latin nouns equus and equitatus, meaning “horse” and “horse riding,” respectively. N. equitans is too small to ride a horse: it is riding as a symbiont on other archaea in the genus Ignicoccus. Ignicocci (such as I.  islandicus and I. hospitalis) are sphere-shaped hyperthermophiles, (extremophiles, typically growing at 80 °C (176 F), but also at higher temperatures); hence the association that N. equitans is riding the fire sphere.

The symbiotic relationship between these two types of archaea has been described as N. equitans parasites attached to the surface of their Ignicoccus host. The parasites are living off the metabolism of its host. N. equitans lacks genes for its own metabolism, but possesses genes for DNA repair and reproduction. It has a highly compact genome—the smallest microbial genome sequenced to date [3,4].

N. equitans was discovered in 2002 by Karl Otto Stetter of the University of Regensburg (Bavaria, Germany), while exploring hydrothermal vents of the Kolbeinsey Ridge [1,2],  a stretch of the Mid-Atlantic Ridge named after a submarine volcano north of Iceland [5]. Stetter is responsible for the name Nanoarchaeum equitans.
 
Keywords: microbiology, nanobiology, archaeal kingdom Nanoarchaeota, hyperthermophile, crenarchaeon, nomenclature.

References and more to explore
[1] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007.
[2]  Microbe Wiki: Nanoarchaeum equitans [biowiki.kenyon.edu/index.php/Nanoarchaeum_equitans].
[3] E. Waters et al.: The genome of Nanoarchaeum rquitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA October 2003, 100 (22), pp. 12984-12988 [www.ncbi.nlm.nih.gov/pmc/articles/PMC240731].
[4] K. S. Makarova and E. V. Koonin: Evolutionary and functional genomics of the Archaea. Curr. Opin. Microbiol. October 2005, 8 (5), pp. 586-594 [www.ncbi.nlm.nih.gov/pubmed/16111915].
[5] Global Volcanism Program > Kolbeinsey Ridge: www.volcano.si.edu/world/volcano.cfm?vnum=1705-01=.

The adjective postprandial, meaning “after eating a meal”

The adjective postprandial ist derived from the Latin noun prandium meaning “meal” or “breakfast.” Hence, postprandial means “after eating a meal” or “after having breakfast.” The adjective preprandial means the opposite—“before eating a meal.”

This adjective appears in medical terms such as postprandial hyperglycemia (high blood sugar after a meal) and postprandial hypotension (excessive decrease in blood pressure after eating) [1-3].

Your pre- and postprandial states are regulated by the two hormons ghrelin and leptin, telling your brain that you should eat and stop eating, respectively. In her review on the recent research of the bacterial network in human bodies, Jennifer Ackerman explains that the bacterium Helicobacter pylori, which thrives in the acidic stomach environment, is responsible for your ghrelin level: people with H. pylori experience a postprandial decrease in ghrelin, while those lacking the bacterium do not and continue to have appetite [4].  In other words: if you apply antibiotics to reduce H. pylori-induced ulcers, you are going to interfere with your postprandial hormon levels and your appetite and, hence, may gain weight. So, use your postprandial time wisely to plan your future eating and treating habits.

Keywords: Latin, terminology, nutritional planning, human body regulation, physiology, medicine.

References and more to explore
[1] Medical dictionary: postprandial [www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=postprandial]
[2]  Medscape Education: Introduction: Clinical significance of postprandial hyperglycemia [www.medscape.org/viewarticle/491410].
[3] Home Health Handbook: postprandial hypotension [www.merckmanuals.com/home/heart_and_blood_vessel_disorders/low_blood_pressure/postprandial_hypotension.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

A gut bacterium named after Greek letters: Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a Gram-negative anaerobic microbe of the human intestinal tract [1].  The specific epithet of this scientific species name is derived from a combination of the three Greek letters theta, iota and omicron (see example in Names of species section in [2]). Curious about taxonomy, Mark Isaak provides amazing listings of diverse and interesting species and their sometimes odd names, but he admits he does not know why those letters were chosen to denote B. thetaiotaomicron [3].

Jennifer Ackerman writes that this term “sounds like it was named after a Greek sorority or fraternity” [4]. We still wonder why θ, ι and ο? More interesting than its name  is the role this bacterium plays in our intestinal tract. Ackerman reports the latest research results on how microbial genes benefit their human hosts and explains how B. thetaiotaomicron produces enzymes that are not encoded within the human genome. B. thetaiotaomicron “assists” us in digesting complex carbohydrates from plant foods: this bacterium “has genes that code for more than 260 enzymes capable of digesting plant matter, thus providing humans with a way to efficiently extract nutrients from oranges, apples, potatoes and wheat germ, among other food” [4]. B. thetaiotaomicron encodes more enzymes than there are Greek letters for.

Keywords: microbiology, microbial biorealm, nomenclature, terminology.

References and more to explore
[1] Microbe Wiki: Bacteroides thetaiotaomicron [microbewiki.kenyon.edu/index.php/Bacteroides_thetaiotaomicron].
[2] J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature   [www.bacterio.cict.fr/foreword.html].
[3] Mark Isaak: Curiosities of Biological Nomenclature [www.curioustaxonomy.net/etym/acronyms.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

Ochoa enzyme, named for the Spanish-American biochemist Severo Ochoa

The Ochoa enzyme is named for the Spanish-American biochemist Severo Ochoa (1905-1993), who was awarded the Nobel Prize in Physiology or Medicine 1959, jointly with Arthur Kornberg,  for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid [1-4].

Severo Ochoa was born in 1905 in Luarca, Spain, and died in Madrid in 1993. He worked, researched, taught and inspired others at various prestigious institutions in Spain, Germany and the Unites States [2].

The Ochoa enzyme, polynucleotide phosphorylase, was first isolated from the bacterium Azotobacter vinelandii [3]. The enzyme synthesizes RNA from ribonucleotide triphosphates. The Ochoa enzyme played a critical role in deciphering the genetic code: the American biochemist Marshall Nirenberg and Heinrich Matthaei (a postdoctoral researcher from the University of Bonn in Germany) used the Ochoa enzyme in the enzymatic synthesis of RNA, which they introduced into Escherichia coli [4,5]. Their work resulted  in an understanding of which three-nucleotide codon in a nucleic acid sequence specifies a particular single amino acid. Thanks to the Ochoa enzyme, they achieved the goal of the RNA Tie Club, whose members were corresponding with each other by amino-acid nicknames.

Keywords: history of science, biochemistry, enzymology, synthetic polynucleotides, mRNA sequences, proteins.

References and more to explore
[1] Nobelprize.org - The Official Web Site of the Nobel Prize: The Nobel Prize in Physiology or Medicine 1959 [www.nobelprize.org/nobel_prizes/medicine/laureates/1959].
[2] Ellen Dubinsky: Severo Ochoa (1905-1993). Washington University School of Medicine, Bernard Becker Medical Library [beckerexhibits.wustl.edu/mig/bios/ochoa.html].
[3] Laurence A. Moran: Nobel Laureate: Severo Ochoa. October 1, 2008 [sandwalk.blogspot.com/2008/10/nobel-laureate-severo-ochoa.html].
[4] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 69.
[5] Profiles in Science: The Marshall W. Nirenberg Papers [http://profiles.nlm.nih.gov/ps/retrieve/Narrative/JJ/p-nid/22].

Corresponding with an amino-acid nickname

Many of us are living and socially interacting with their nicknames. But can you image to use the name of an amino acid as your nickname—or worse, its associated three-letter code? That 's exactly what the members of the RNA Tie Club did  [1-3]: This club was founded in 1954 by the Russian physicist George Gamow, who was interested in the relationship between the molecular RNA structure and protein formation in living cells.

During the 1950s and 1960s it was “hot and hip” (in bioscience and beyond) to speculate about and gain insight into genetic information at the molecular level: the relation between the structure of the DNA strand with its four-letter code and the α-amino acids (see codes and names in different languages) that combine into proteins. Researchers started to realize that RNA, a single-stranded molecule, is playing a key role in this biomolecular translation procedure. To crack the genetic code—now known as the list of amino-acid-encoding three-letter codons of RNA (and DNA)—in a joint effort, the RNA Tie Club was formed. Its members included George Gamow, who was Ala for alanine, Sir Francis Crick (Tyr for tyrosine), James Watson (Pro for proline) and Sydney Brenner (Val for valine).

Each club member received a necktie with the double helix structure and a lapel pin showing his (no females involved) amino acid symbol (hence the club name). The club had 20 members, one for each amino acid of interest (the so-called standard amino acids) and four honorary members representing each nucleotide. Eight members won a Nobel Prize; but not for cracking the code. Ironically, Marshall Nirenberg and Heinrich Matthaei, the scientists who successfully deciphered the genetic code by clever experiments in 1961, were not members of the club. Obviously, the club gentlemen did not participate in the hands-on deciphering race as much as they enjoyed smoking, drinking, tie-binding and hypothesizing.   

 The last time I checked the Wikipedia RNA-Tie-Club page (en.wikipedia.org/wiki/RNA_Tie_Club, also see [2]) I found a table with all club members, their amino-acid designation and their training. Interestingly, only half of them were biologists or chemists, while the others came from a physics and mathematics background.

Keywords: history of science, biochemistry, molecular biology, scientific gentlemen's club, humor, anecdotes.

References and more to explore
[1] Nobelprize.org - The Official Web Site of the Nobel Prize: How the Code was Cracked. What Code? [www.nobelprize.org/educational/medicine/gene-code/history.html].
[2] Power of the Gene > History of Genetics > The RNA Tie Club [powerofthegene.com/joomla/index.php/jistory-of-genetics/the-rna-tie-club]. 
[3] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 68.

A term in microbiology: archaea, shortened from archaeabacteria to denote the third domain

In 1977, when Carl Woese and George Fox reformulated the prokaryote-eukaryote grouping as a result of their phylogenetic analysis based upon ribosomal RNA sequencing, they proposed three main branches for the tree of life: eubacteria (typical bacteria), archaebacteria (then only methanogenic bacteria) and urkaryotes that evolved into components of eukaryotic cells [1].  Now these three domains are named bacteria, archaea and eukarya, respectively. Animals, plants and fungi, for example, branch of as subdomains from the latter.

The name archaea was introduced in 1990 by Woese as a short form of the term archaeabacteria [2]. The intention further was to eliminate the bacteria connotation, since archaea significantly differ from “typical” bacteria.

Although the three-domain system finds wide acceptance today, this bacteriocentric scheme has also been critized since it fails to recognize cell symbiogenesis—a five-kingdom scheme has been suggested instead [3].

Archaea are now known to fill many places of our world (at least on Earth). They are thriving in harsh environments, but also in soils, swamps and animal colons. A peer-reviewed, open-access journal with the title Archaea exists in which research and review articles are published that cover topics in archaea biology, ecology and bioinformatics  [4].

Keywords: microbiology, three-kingdom system, phyla of life, taxonomy, nomenclature.

References and more to explore
[1] Carl Wose and George Fox: Phylogenetic structure of the prokarotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA November 1977, 74 (11), pp. 5088-5090 [www.pnas.org/content/74/11/5088.full.pdf].
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 60-61 and 86.
[3] Lynn Margulis and Karlene V. Schwartz: Five Kingdoms. Henry Holt and Company, New York, Third Edition 1998.
[4] Hindawi Publishing Corporation: Archaea [www.hindawi.com/journals/arch/].