14 TIBS 14 - January 1989

Letters A surprising omission

Whilst reading the recent article by Saimi et al. ' Ion channels in Parame- cium, yeast and E. coli '~ we were rather surprised by the omission of the best known bacterial ion channels, the porins. These are the major proteins of the E. coli outer membrane and gener- ally exist at copy numbers of up to 100 000 per cell (2% of total protein). Transport studies have shown that they are almost solely responsible for the permeability properties of the outer membrane. Since the pioneering work of Benz et al. 2 and Schindler and Rosenbusch 3 in 1978, single channel data has been collected on at least six E. coli porins whilst similar channels have been shown to exist in other Gram-negative species. The experi- ments show that porins vary in speci- ficity from the weakly cation selective OmpF to the maltose-specific LamB and have single channel conductances of between 150 and 2000 pS in l M KCI.

Excellent reviews of this work have been written by Nikaido and Vaara 4, Benz 5, Brass ~' and others.

The paper suggests that one of the channels found by the patch-clamp technique occurs in the outer mem- brane and possibly regulates the con-

tent of the periplasmic space. In this particular case the lack of comparison with porin is surprising. However, for a review with the above title to com- pletely ignore over fifteen years of gen- etics, biochemistry and biophysics on the major ion channels of E. coli is nothing short of incredible.

References 1 Saimi, Y., Martinac, B., Gustin, M. C.,

Culbertson, M. R., Adler, J. and Kung, C. (1988) Trends Biochem. Sci. 13,304~309

2 Benz, R., Janko, K., Boos, W. and L/Auger, P. (1978) Biochim. Biophys. Acta 51 l, 305- 319

3 Schindler, H. and Roscnbusch, J. P. (1978) Proc. NatlAcad. Sci. USA 75, 3751-3755

4 Nikaido, H. and Vaara, M. (1985) Microbiol. Rev. 49, 1-25

5 Benz, R. (1985) CRC Crit. Rev. Biochern. 19, 145-190

6 Brass, J. M. (1986) Curr. Top. Microbiol. lmmunol. 129, 1-92

JEREMY LAKEY

FRANC PATTUS

European Molecular Biology Laboratory,

Postfach 10.2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.

Reply from Saimi et al.

We agree with J. Lakey and F. Pattus that porins should have been men- tioned in our article (1988, TIBS 13, 304-309). We intended to review E. coli channels found by patch-clamp studies only and so far porins have not been studied by use of this technique. (Note, however, that in a footnote we did cite a review on porins by Hancock [1987, J. Bacteriol. 169,929-933] with reference to channel pore size.)

The original article (Martinac et al. 1987, Proc. Natl Aead. Sci. USA 84, 2297-2301) on which the E. coli portion of our TIBS article was based, contains a lengthy discussion on porins as studied by previous authors. We cited the work of Benz, Nakae, Nikaido, Rosenbusch, Schindler, and their co- workers.

How the ion channels found by patch-clamp studies relate to porins is being dealt with at length in a manu- script in preparation.

YOSHIRO SA1MI M.R. CULBERTSON

BORIS MARTINAC JULIUS ADLER

MICHAEL C. GUSTIN CHING KUNG

Laboratory of Molecular Biology, University of Wisconsin, Madison, W153706, USA.

A sequence editor for microcomputer users

A recent Microfile column (TIBS 13, 321-324) described two multiple sequence editors for use with minicom- puters. Microcomputer users need not feel left out because I have written a similar editor, ESEE, that runs on IBM-PC and compatible microcom- puters. The current release of ESEE can accommodate up to 21 16-kilobase sequences and it incorporates most of the common features of a modern word processor as well as a host of functions specific to sequence analysis. Another important function of ESEE is to act as an intermediate between the currently available sequence analysis packages which are notoriously unable to com- municate with one another.

ESEE, an online help file and a manual are available on disk for a nominal fee that covers shipping, hand- ling and updates. Interested readers should contact me.

ERIC CABOT

Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada V5B 1 $6.

Response to Price's protein puzzle

I didn't write before, in reponse to Price's protein puzzle (TIBS 12, p, 349) to find the longest word in any known protein sequence, because a six-letter word didn't seem very impressive to me. I expected eight- or nine-letter words to be the winners. So, there it is:

96 101 A L L E L E Ala Leu Leu Glu Leu Glu

which is a part of a complement pro-

tein, C1R-B. The main reference is Sim, R.B. etal. (1977) Biochem. J. 163, 219-227, as quoted by Kabat, E.A. et al. (1987) in Sequences o f Proteins o f Immunological Interest, 4th Edn, p. 389, National Institutes of Health.

By reading the sequence in several possible 'reading frames', the following succession of words can be found:

94 96 97 100101 103 D I A L

A L L E L E L E N S

which can be considered 'curiouser and curiouser ' , specially because it has such 'biological ' words as A L L E L E and LENS in it.

Servicio lnmunologia, Hospital La Paz, P° de la Castellana 261 28046 Madrid, Spain.

ADOLFO JIMENEZ