UniProt release 2012_01

Headline

What’s in a (species) name?

Carl Linnaeus, the father of taxonomy, was responsible during his life for the naming of nearly 8,000 plants, many animals and the scientific designation for humans: Homo sapiens. Linnaeus used many of his supporters and detractors as inspiration for naming plants. The most beautiful plants were often named in honor of his supporters while his detractors often supplied the names of common weeds or unattractive plants. Rather like an artist signing a painting, Linnaeus signed all his descriptions, his signature becoming over the centuries a simple L followed by a point. Sober. Even to this day taxonomically approved names may use this idea, but less soberly; the red alga Gracilaria chilensis was discovered in 1986 by C.J. Bird, J. McLachlan & E.C. Oliveira, giving us Gracilaria chilensis C.J. Bird, J. McLachlan & E.C. Oliveira, 1986.

Linnaeus advocated the use of commemorative personal names as botanical names. In ‘Critica Botanica’, he commented with humor about the naming of Linnaea borealis: “It is commonly believed that the name of a plant which is derived from that of a botanist shows no connection between the two… [but]... Linnaea was named by the celebrated [Jan Frederik] Gronovius and is a plant of Lapland, lowly, insignificant, disregarded, flowering but for a brief space – after Linnaeus who resembles it”. It may not be an excessively objective statement.

Thunbergia was named in 1780 by Retzius in honor of Carl Peter Thunberg (1743-1828), the Swedish naturalist, and perhaps the greatest pupil of Linnaeus. Kosteletzkya for Vincenz Franz Kosteletzky (1801-1887), Bohemian physician and botanist. Jacobsenia for Hermann Johannes Heinrich Jacobsen (1898-1978), German botanist and curator at Kiel botanic garden… there are many, many more examples.

Latin is still necessary at least to understand the species epithet. Ehrharta longiflora, longiflora referring to the elongate flowers of this species. And Ehrharta? J.F. Ehrhart (1742-1795) was a German botanist, yet another of Linnaeus’ pupils.

Sometimes scientific names bear the names of people who described the species or were instrumental in discovering them. Several archaeabacteria have been named in honor of Carl Woese (1928-), famous for defining the archaea in 1977, such as Pyrococcus woesei, or Methanobrevibacter woesei or Conexibacter woesei.

Euzebya tangerina, tangerine-colored bacterium was named in 2010 after Jean-Paul Euzéby, a French microbiologist who has contributed significantly to microbial systematics, including the Latinization of microbial names.

And Przewalskium albirostris? The Latin etymology of the name suggests that this creature has a white beak (albus: white and rostrum: beak, trunk or proboscis), or a white-lip. It was formerly named Cervus albirostris. Cervus means deer!! Now we know: it is a white-lipped deer. But it was renamed Przewalskium albirostris after N.M Przhevalsky (1839-1888), a Russian geographer.

In view of the names cited above, you may have the feeling of attending a popularity contest in the scientific community, but other kinds of tribute are also possible: a pheasant was named Chrysolophus amherstiae to commemorate Sarah Countess Amherst who sent the first specimen to London in 1828. In a more recent past, a newly discovered bacterium was named Midichloria mitochondrii. Does Midichloria remind you of anything? Schoooooooooooooooo…Luke, I am your father. Midichloria, a gram-negative bacterium, takes its name from the Star Wars microbes, midi-chlorians, which grant the Jedi and the Sith the ability to use the Force. In real life, Midichloria mitochondrii are non-obligate symbionts that reside primarily in the mitochondria.

Of course the appreciation of people deserving a tribute remains questionable. A nice cactus has been called Rebutia einsteinii, but there is no Opuntia oppenheimerii Why not oppenheimerii? Why a cactus? We leave the question open for the future generations of taxonomists.

UniProtKB news

Changes to the controlled vocabulary for PTMs

New term for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):

• 5-hydroxy-3-methylproline (Ile)

Deleted term:

• 5-hydroxy-3-methylproline

Website news

Clustal Omega replaces Clustal W as UniProt’s protein alignment program

We have upgraded the alignment web service used to align protein sequences in UniProt from Clustal W to Clustal Omega. This has been made possible with the help of a new bioinformatics analysis tools framework at EMBL-EBI. Clustal Omega is the latest addition to the Clustal family of programs. It offers a significant improvement upon Clustal W in the following areas:

• Accuracy – Better quality protein sequence alignments.

• Scalability – Better at aligning larger numbers of sequences.

• Speed – Faster alignments, making use of multiple processors where present.

Clustal Omega is currently only suitable for aligning protein sequences and not DNA or RNA sequences.