Compilation of DNA sequences of Escherichia coli (update 1991)

© 1991 Oxford University Press Nucleic Acids Research, Vol. 19, Supplement 2023

Compilation of DNA sequences of Escherichia coli(update 1991)

Manfred Kroger*, Ralf Wahl and Peter Rice1

Institut fur Mikrobiologie und Molekularbiologie, Fachbereich Biologie, Justus-Liebig-Universitat GieBen,Frankfurter Strafie 107, D-6300 GieBen and 1EMBL, Postfach 10.2209, Meyerhofstr.1, D-6900Heidelberg, FRG

ABSTRACT

We have compiled the DNA sequence data for E.collavailable from the GENBANK and EMBL data librariesand over a period of several years independently fromthe literature. This Is the third listing replacing andincreasing the former listing roughly by one fifth.However, in order to save space this printed versioncontains DNA sequence information only. Thecomplete compilation Is now available in machinereadable form from the EMBL data library (ECD release6). After deletion of all detected overlaps a total of 1492 282 individual bp Is found to be determined till thebeginning of 1991. This corresponds to a total of31.62% of the entire E.coll chromosome consisting ofabout 4,720 kbp. This number may actually be higherby some extra 2,5% derived from lysogenlcbacteriophage lambda and various DNA sequencesalready received for statistical purposes only.

INTRODUCTION

Within this sequence supplement issue we were able to publisha compilation of DNA sequences of Escherichia coli both in 1989and 1990 and asked our colleagues from all over the world foradditions and corrections [1,2]. Ever since the number of newlypublished E.coli sequence data increased substantially (seeTable 1). Thus we were able to add and correct a number ofentries. According to our data a total of 1 492 282 bp is sequencedtill January 1991. At least one third of the nucleotides is publishedtwice. The data presented here may serve as a basis forencouragement to our colleagues to either send us theirunpublished, mostly flanking material or to determine additionallythe sometimes very small gaps towards known neighbouringsequences. This may finally help to produce the Escherichia coliK12 DNA sequence as the first complete sequence of a livingorganism. This compilation is available in its complete formquarterly from EMBL data library together with their currentrelease on tape (ECD). It may also be received on CD-ROMtogether with a service stand alone program for quick databasesearch and direct access to collected sequences.

PREVIOUS AND SUPPORTING EFFORTS

The most famous collection of E.coli data is the linkage mapcompiled by B.Bachmann [3]. These data were recently updatedand we tried to follow this update as much as possible. Threeother groups [4 — 8] started a program to fit the DNA sequencedata directly onto the physical map compiled by Y.Kohara et al.[9]. We preferred the genetic map positions rather then thephysical map coordinates, since we try to include genetic dataas well. In general one may obtain the physical data simply bymultiplying the genetic 'map' data by a factor of 47.2. Thisoperation needs to pay attention to a large inversion within theKohara restriction map, which however is considered in two othercosmidbanks [10,11]. In order to be prepared for merging ourdata with those regarding the Kohara map data directly [4 — 8]we have compared our data and paid attention to all of thesecollection as far as possible. Only the unpublished material (about68 000 bp) available exclusively to us, to K.Rudd or to B.Baum(both Bemesda, MD) is not included into the collection presentedhere, but may be available on personal request. Additions andcorrections of several colleagues are indicated in the main listwithin the comment column (see Table 1 for abbreviations).

PERFORMED COMPILATION

The general scope of this collection is to allow a compilationof all uncoordinated sequence information to finally end up witha complete Escherichia coli nucleotide sequence data bank,including all sequenced mutants. In order to give a visualimpression about the availability of sequence information of E. coliDNA we include an appropriate figure. This Figure 1 is printedautomatically on a high resolution printer and is to scale as faras possible. The extent of the black bars represents the mainlysequenced areas. All sequences with more then 2000 contiguousbasepairs are shown. The final print may not give enoughresolution, thus the comparison with the main list is stronglyrecommended.

Besides the pure sequence information some specified additionsare introduced, mostly if restriction maps could be found in theoriginal paper. We used B.Bachmann's genetic map data to sortthe sequences roughly by a tenth of a minute. Fine assortmentwas by a hundredth of a minute, if the sequences overlap. A

* To whom correspondence should be addressed

Downloaded from https://academic.oup.com/nar/article-abstract/19/suppl/2023/1058067by gueston 15 February 2018

2024 Nucleic Acids Research, Vol. 19, Supplement

hundredth of a minute corresponds to 472 bp, which seems tobe a sufficient resolution. If the sequences were mapped in eitherof the compilations using the Kohara map [4 — 8], we preferredto use their assignment including the respective orientation.

Note, the given map coordinate may vary somehow withindifferent issues of this collection, due to increasing number ofrecognized overlaps. If the numbers are not consecutive withincollected entries, you may find the missing entries within theelectronic ECD data bank only. Numbers higher then 100 withinthis line refer to DNA sequences, which could not be localizedwithin the chromosome yet. The numbers refer to the followingtype of information:

101 —126 Unlocalized structural genes in alphabetical order> 200 Insertion sequences in quasi numerical order (e.g.

200.05 is IS5; 201.50 is IS150)> 300 tRNAs filed as RNA sequences and unlocalized

tRNA genes in alphabetical order of thecorresponding amino acidsunlocalized RNAsreviews and summaries (neglected here)

>400>500

The gene symbols are either according to the Bachmann list orto the respective paper. Several symbols have been changed inthe past for different reasons. Thus the given entry names withinthe EMBL or GenBank entries differ sometimes from the givengene symbol. These differences are indicated as much as possiblemostly using the ' = ' symbol in the last position of the namecolumn pointing to the comment column. If more then two genesymbols are necessary to describe the content either of a singleor a condensed entry, the '&' symbol points to the commentcolumn, in order to indicate that this area consists of more thantwo genes. Thus the two columns should be read as oneconsecutive item. We tried to use each gene symbol at least oncein the first position. Since a fairly compressed form had to beused within this databank, some terms and abbreviations had tobe used and are explained in Table 1.

This third edition of ECD contains a major increase ofinformation by adding the exact coordinates for the performedoverlaps. In order to make the calculations transparent, wepreferred to keep all references with contributions to therespective area. In future issues we may only be able to quoteone reference per data bank entry. However, the full set ofinformation will always be provided on the electronic ECDversion. Structural information besides the DNA sequence dataand some other functional data, e.g. restriction map data,functional analysis data, sequence corrections or sequencedmutations are now also only in the electronic ECD version. MosttRNA sequences are compiled together with their respectiveanticodon sequence. For crossreferences to the tRNA collection[12] see our previous listing [1]. Most ribosomal operons arenot fully sequenced within their 16S and 23S RNA genes. Thusthe compiled sequences are sometimes only analogs. Insertionsequences are compiled using the known copy number withinE.coli K12 strain W3110 [13,14]. A future issue of this collectionmay contain this information at the respective genetic locus.

Strains other then E.coli K12 are indicated. However, therespective sequence data are not included in the final calculation.Names not found within the Bachmann list or not geneticallydefined within the original paper are abbreviated but explainedwith the full name. Undetermined or open reading frames (urfor orf) are indicated mostly according to the original paper andthe resulting protein size. Regions with no specific genetic

function are marked as intergenic or flanking regions. Somereviews on the genetic or functional structure as well as on cosmidbanks are included, but neglected here.

The accession number column gives the first accession numberfor any EMBL entry. This number remains constantly with thequoted nucleotide sequence. It is therefore the most importantcross reference. According to the general databank policies theaccession number will even be part of any condensed entry afterremoving overlaps. Thus an EMBL EC entry may be found viadifferent accession numbers, but each accession number pointsto one individual EC entry only. If the EMBL-accession numberdiffers from the GenBank accession number, the GenBankaccession number is given in the comment column.

The EMBL column gives the EMBL entry name for the givenreference, usually beginning with the identification EC Therespective GenBank entry name usually begins with ECO ,and is given in the respective column. This may be used to findEscherichia coli sequences directly either within the EMBLdatabank or GenBank. However, this identification may also pointto plasmid borne and other sequences (for a list of these entriessee the previous listing [1]).

Note, that the EC or ECO entry name may have been changedbetween different database releases, especially due to compressingoverlapping sequences or to changing preliminary names (usuallythe respective accession number). Numbers in brackets after thename point to the position of this reference within the list ofreferences of the respective GenBank/EMBL entry. Incorporationof these numbers is still incomplete. In order not to depend onthese changes the respective invariant accession number is alwaysgiven in the accession number column.

There are now five columns giving different types of numbersof basepairs:

1) The basepair ('bp') column gives the number of basepairsfound in the reference quoted. The number is mostly consistentwith the respective number given in the EMBL or GenBank entry.If it is clear from the original text, that the given sequenceinformation is used as illustration only and not originallydetermined here, the entry within this column is 0. If the textallows to complete restriction sites the flanking nucleotides areadded, or if it allows to recognize vector sequences, thesesequences are omitted. Thus the given number may differ fromthe EMBL or GenBank entry. This is mostly indicated in thecomment column.

2) The 'offset' column is a control number for ascending orderin the map column and describes the number of nucleotidescollected up to the previous entry.

3) The 'from' column defines the address number of thenucleotide to begin with in the respective collection.

4) The 'to' column defines the respective nucleotides toterminate the respective collection. If the from number is higherthen the to number our program automatically inverses thesequence.

5) The total column gives the number of basepairs added toa total number after deletion of all repeats and overlaps fromdifferent entries. This number is given only once per added areain the first entry after a sort by the genetic map position. Datafrom strains other than E.coli K12 are ignored in this calculation.If there is no overlap to other entries the numbers given in thebp and total column are identical. Adding up all entries in thiscolumn we arrive at the actual number of sequenced basepairsof the entire E. coli genome. The actual number of total basepairssequenced up to January 1991 is 1 492 282 bp = 31.6%


Nucleic Acids Research, Vol. 19, Supplement 2025

In order to distinguish between the different entries, e.g.forthis printed version of the data base, an additional one lettercolumn (•) is included as well. T defines the start of a completelycollectable entry. P defines the start of an entry only partiallycollectable. F defines an entry missing in the EMBL data base.C defines any collectable entry other then the starting one.B, J, U, and YV define entries from strains other then E.coli K12.The article column line gives the references for the quotedsequence information in a fairly condensed format and indicatesthe volume and first page of each entry, only. The appropriateyear is added in a special year column to allow the calculationof an annual index given in Table 2. A list of abbreviations forthe respective journals is given in Table 3.

DATA DISTRIBUTION IN MACHINE READABLE FORM

This compilation is available as a flat file (ECD) from the EMBLdata library and is automatically distributed with the each releasethe EMBL data library. In addition, this compilation is availabletogether with a stand alone service program on the CD-ROMversion of the EMBL Hata library, but this version is also availableon disk on request from Gie/3en. Both versions including theservice program are available from the EMBL file server [15].Using this program one may assemble the entire nucleotidesequence directly from the CD-ROM or may extract each singleor collected entry individually.

ACKNOWLEDGEMENTS

We like to thank Kenn Rudd (Bethesda) for his unpublishedlisting, and Peter Stoehr, David Hazeldine and Rainer Fuchs(EMBL) for constant flow of recent database additions. This workis supported by the Deutsche Forschungsgemeinschaft (SFB 272).

REFERENCES

1. M.Kroger, Nucl.Acids Res. 17 (Suppl.), r283-309 (1989)2. M.Kr6ger, R.Wahl and P.Rice, Nucl.Acids Res. 18 (Suppl.) 2549-2587

(1990)3. B.J.Bachmann, Microbiol. Rev. 54, 130-197 (1990)4. K.E.Rudd, W.Miller, J.Ostell and D.A.Benson, Nucl. Acids Res. 18,

313-321 (1990).5. C.Mecligue, J.P.Bouche', A.Henaut and A.Danchin, Molecular Microbiology

4, 169-187 (1990)6. C.Metligue, A.Hdnaut and A.Danchin, Molecular Microbiology 4,

1443-1454 (1990)7. H.Watanabe and T.Kunisawa, Protein Seq. & Data Analysis 3, 149-156

(1990)8. T.Kunisawa, M.Nakamura, H.Watanabe, J.Otsuka, A.Tsugita, L.-S.L.Yeh,

D.G.George and W.C.Barker, Protein Seq. & Data Analysis 3, 157-162(1990)

9. Y.Kohara, K.Akiyama and K.Isono, Cell 50, 495-508 (1987).10. R.P.Birkenbihl and W.Vkdmetter, Nucleic Acids Res. 17, 5057-5069 (1989).11. V.Knott, DJ.Blake and G.G.Browlee, Nucl.Acids Res. 17, 5901 -5912

(1989).12. M.Sprinzl, T.Hartmann, J.Weber, J.Blank and R.Zeidler, Nucl.Acids Res.

17 (Suppl.), r l -172 (1989)13. M.Umeda and E.Othsubo, J.Mol.Biol. 208, 601-614 (1989)14. R.P.Birkenbihl and W.Vielmetter, Mol.Gen.Genet. 220, 147-153(1989).15. P.J.Stoehr and R.A.Omond, Nucl.Acids Res. 17, 6763-6764 (1989).



malFEKBrrnK

rpoBCrrnB

lleShsdRHS I e n VA

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80

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rrnD

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4 720 000 bp

January 30, 1991

pheST

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Fig . l The sequenced areas within the circular chromosome of Escherichia coli K12. The sequenced areas are calculated in percent of the total chromosome accordingto the main list. All sequences exceeding 2000 bp are shown as in scale black bars at the respective genetic map position. Some prominent markers are included as well.



Table 1. Databank cross references and abbreviations. Some differences between the two databases or repeated entries, as well as accession numbers given in mostrecent papers are indicated directly.

Gb points to a difference mostly in the accession number between GenBank and EMBL databanks [see also AC line].GbNew is introduced, if the actual issue of GenBank data bank may not contain this more recent entry. However, caused by a certain difference in

updating these entries, they may already be incorporated into the most actual GenBank version. They are always available using theEMBL/GenBank file server.

KR indicates entries primarily found by K. Rudd [3]BB acknowledges the contribution of Bobby Baum, 6607 Pyle Road Bethesda, Maryland 20817, USA. Entries marked by BB are added [new] or

corrected [length, map location, overlap] using a listing compiled by Bobby Baum. His collection may be available as Ec.lis file via theNational Biomedical Research Foundation (USA).

MK [Manfred Kroger] andHD [Peter Rice or other colleagues at EMBL] point to unresolved differences to the databases found by these individuals,char characterization of genetic elementscomp comparison with other organismscorr correction of published datafunc functional descriptiongap small undetermined gapsmap restriction or genetic map datamut sequenced mutationsprom characterized promoter sequencesregul characterized regulatory sequencessumm summation or reviewunpub unpublished material quoted in the respective article or in the database

Table 2. Annual growing of the E.coli DNA-sequence information. This table represents all included sequence information. The final number for total informationexceeds the actual number of sequenced nucleotides (1 492 282 bp) roughly by one third.

Yearannualentries

totalentries

annualinformation (bp)

60020534924984142643420582053011166670

20077362221157128138213175317884415918324643220345724834928599332687526507

totalinformation (bp)

60080511541403224426703104330941294659577512445325226874418445626583839759157643573561898205011855071433856171984920467242073231

1967196819691970197119721973197419751976197719781979198019811982198319841985198619871988198919901991

124310564979

214155759312513715517014817919422911

13710202531354451608112217725234547060776293210801259145316821693



Table 3. List of abbreviations for journals

ABB Archives of Biochemistry and BiophysicsAcMB Archives of MicrobiologyAdER Advances in Enzyme RegulationAgrB Agricultural Biochemistry (Tokyo)AEMb Applied Enviromental MicrobiologyAnMi Annales of MicrobiologyANYA Annales of New York Academy of ScienceBBA Biochemica Biophysica ActaBBRC Biochemical Biophysical Research CommunicationsBChF Biochemie (France)BiCh Biochemistry (USA)Bint Biochemistry InternationalBiRp Bioscience ReportBJ Biochemical Journal (UK)Bioo Bioorganic Chemistry (UdSSR)CJMi Canadian Journal of MicrobiologyCRC Carlsberg Research CommunicationCSHQ Cold Spring Harbour Symposium of Quantitave BiologyCell CellDANs Doklady Akademia Nauk (UdSSR)DNA DNAEJB European Journal of BiochemistryEMBO EMBO JournalFEBS FEBS LettersFedP Federation ProceedingsFEMS FEMS Microbiological LettersG GeneticsGAnT Gene Analysis TechniquesGene GeneJBCh Journal of Biological ChemistryJBac Journal of BacteriologyJBio Journal of Biochemistry (Japan)JCBc Journal of Cellular BiochemistryJGMi Journal of General MicrobiologyJMAG Journal of Molecular and Applied GeneticsJMB Journal of Molecular BiologyMBE Molecular Biology and EvolutionMGG Molecular General GeneticsMiRV Microbiological ReviewsMoMB Molecular MicrobiologyN NatureNAR Nucleic Acids ResearchNNB Nature New BiologyPNAS Proceedings of the National Academy of Science (USA)Prot PROTEINS: Structure, Function and GeneticsPSDA Protein Sequences and Data AnalysisScie ScienceUnpub. unpublished material quoted in the databanksZNfC Zeitschrift fflr Naturforschung Part C (Biological Sciences)



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Documents

Compilation of DNA sequences of Escherichia coli (update 1991)