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Phylogenetic Status of Sporosarcina Ureae

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Phylogenetic Status of Sporosarcina Ureae INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1976, p. 305-310 Vol. 26, No. 3 Copyright 0 1976 International Association of Microbiological Societies Printed in U.S.A. Phylogenetic Status of Sporosarcina ureae KENNETH J. PECHMAN, BOBBY J. LEWIS, AND CARL R. WOESE Department of Genetics and Development, University of Illinois, Urbana, Illinois 61801 The phylogenetic position of Sporosarcina ureae was reexamined by “compar- ative cataloging” of its 16s ribosomal ribonucleic acid. The data were analyzed in the context of similar information for Micrococcus luteus (Sarcina lutea), . Bacillus pasteurii, B. subtilis, and B. stearothermophilus. It is concluded that S. ureae is best classified as a member of the genus Bacillus in the same subgroup as is B. pasteurii. The taxonomic position of Sporosarcina MATERIALS AND METHODS ureae has been historically controversial: in the S. ureae ATCC 6473 was purchased from the seventh edition of Bergey’s Manual (21, it is as- American Type Culture Collection, as was B. pas- signed to the genus Sarcina in the family Mi- teurii ATCC 11859. Micrococcus luteus (Sarcina lu- crococcaceae, whereas in the most recent edi- tea UIMD 701) was obtained from the Microbiology teaching laboratory at the University of Illinois. tion it is placed in the family Bacillaceae (3). Organisms were labeled with :3’P0,in a low-phos- The controversy originates from the fact that phate medium, i.e., yeast extract-peptone medium the vegetative cells of S. ureae resemble those from which most of the phosphate had been removed of species in the genus Micrococcus in their by precipitation as magnesium-ammonium phos- shape, cell wall composition, and mode of divi- phate (11). To facilitate growth of S. ureae and B. sion, but produce endospores (5) and possess a pasteurii, this medium was supplemented with urea deoxyribonucleic acid (DNA) having a guanine (final concentration, 0.3 M) and adjusted to a final plus cytosine content typical of that of the fam- pH of 8.5 (4, 5,8). Otherwise, procedures for labeling ily Bacillaceae (1). Detailed study of these the organisms and extracting and purifying the spores (6, 9, 14, 16) has shown that their size, RNA were as described elsewhere (15, 19; K. J. Pechman, Ph.D. thesis, Univ. of Illinois, Urbana, shape, chemical composition, heat resistance, 1975). ultrastructure, and germination properties re- Labeled 16s rRNA was characterized in terms of semble those of Bacillus spores. Biochemically, its oligonucleotide fingerprint as described previ- S. ureae resembles species of the genus Bacillus, ously (13, 17). Basically, this procedure is as follows. especially B. pasteurii (10). Jensen and Sten- A fraction of “2P-labeled 16s rRNA is digested with mark (71, characterizing the control of the 3- T1 ribonuclease, and the resulting products are sep- deoxy-D-arabino heptulosonate 7-phosphate syn- arated by two-dimensional paper electrophoresis. thetase, showed unequivocally that the control Oligonucleotide spots on the resulting electropho- retogram (whose sequences are not obvious from in S. ureae resembles that in the genus BacilZus their positions) are then sequenced, by a combina- but not in the genus Micrococcus. In addition, tion of “secondary” and “tertiary” enzymatic proce- nucleic acid hybridization studies using ribo- dures, producing a sufficient variety of overlapping nucleic acid (RNA) from S. ureae and DNA digestion products in each case to permit the deduc- from various bacterial sources indicate that S. tion of sequence (17, 18). ureae is more closely related to the family Bacil- laceae than to the family Micrococcaceae (8). RESULTS In the present study, comparative oligonu- cleotide cataloging of 16s ribosomal RNA Table 1 presents the 16s rRNA oligonucleo- (rRNA) is used to examine the phylogenetic tide catalogs for the three organisms M. luteus, position of S. ureae. The results indicate une- S. ureae, and B. pasteurii. The presence or quivocally that S. ureae is closely related to the absence of these oligonucleotides in the 16s genus Bacillus. In particular, S. ureae is found rRNA of B. subtilis and B. stearothermophilus to be more closely related to B. pasteurii than (18) is also indicated to provide additional per- are other species of the genus Bacillus exam- spective. Only oligonucleotides (pentamer and ined to date. Hence, s. ureae is probably best larger) are listed, since the smaller ones, regarded as a member of the subgroup of the which tend to occur in multiple copies, have no genus Bacillus which contains B. pasteurii significance here (12). Table 2 summarizes the rather than as a separate genus within the oligonucleotide coincidences found among the family Bacillaceae . various organisms. 305 306 PECHMAN, LEWIS, AND WOESE INT . J. SYST.BACTERIOL. TABLE1. Tabulation of characteristic T1 ribonuclease-generated oligonucleotide sequences for Micrococcus luteus, Sporosarcina ureae, and Bacillus pasteurii" I Oligonucleotide 'c:'Y 14 u28s 2$g v) S~csai cs Pentamer Octamer CCCCG 100 CCAACCCG CACCG 100 - ACAAACCG CCACG 011 + AACACCAG CCCAG 211 + CAAACCCG 1 ACCCG 011 + CAACG 111++ CCACACUG !I + ACACG 111 + CUCAACCG 1 + ACAAG 0 - - 110 ACAUCCCG 0 ACCCCAUG 0 UCCCG 111 I + + CCCUG 001 - - CCCUUCAG 1 UCACG 100 CCCCUUAG 1 UACCG 111 + CCUAUCAG 0 CUCAG 111 + UCAACUCG 0 ACUCG 100 CUUAACCG 0 - ACCUG 0 2 2-1 + AUACCCUG 1 + UACAG 0 I 1 1-2 - CUACAAUG 1 + UCAAG 1 01 0 -b CUAAG 011 + AAUUCCUG 1 0 0 UAACG 001 + CAAUG 010 + UUCCUUCG 0 lo 1 AUCAG 111 + AUUUAUCG 1 0 0 ACUAG 100 - AAUUAUUG 1 1 1 + AAUCG 011 + ACAUG 110 AUACG 200 Nonamer AACUG 010 CAACCCUCG 0 UAAAG 111++ CUACACACG 1 + AUAAG 100 - UACACACCG 1 + AAAUG 011 + UAACACCCG 1 + CUCACCAAG 1 + CUCUG 011 ++ ACAUCCCAG 1 - CCUUG 1-2 0 0 ++ UCAUG 0 1 0' - CAACCCUUG 0 CUAUG 001 ACUCCUACG 1 UAUCG 011 CUUACCAAG 0 ACUUG 010 + CACUCUAAG 0 AUCUG 100 - CUAACUACG 1 UAUAG 001 - CUAAUACCG 1 UUAAG 3 1-2 1 + AAUUCCACG 1 UAAUG 111 - AUAACUCCG 1 AUUAG 211 ++ (AU, AAU, C, C)AG 0 AAUUG 111 + CCCCUUAUG 1 1 1 + UCUUG 122 + + (CC, U)UUUAAG 0 1 1 UUUUG 100 AUUAAUUCG 1 0 0 Hexamer CCCACG 011 + UUUAAUUCG 0 1 1 + CACAAG 111 + -+ VOL. 26, 1976 PHYLOGENETIC STATUS 3F S. UREAE TABLE1 -Continued Oligonucleotidc Oligonucleotide .U'I) v) s 3 Y 8 8 B Y 'y ; Ly $ B % vj s vj aj - - _. - AAACCG 0 1 1 lecamer AACAAG 0 1 1 AAACUCAAAG 0 1 1 CAAACG 0 0 1 CUUAACCCCG 1 0 0 UCCACG 0 1 0 CUAACG 1 1 0 (AU,ACIAUCAUG 0 1 0 CACUAG 1 0 0 UCUAAUACCG 1 0 0 ACACUG 0 1 0 UAACCCUUAG 0 1 0 UAAACG 1 1 1 CCACUCUAUG 0 1 0 AAUACG 1 1 1 ACUAAG 1 0 0 UUU(CU)CUUUG 0 0 1 AAACUG 1 1 1 AUACAG 0 1 0 Jndecamer ACCAUUCCACG 1 0 0 UUCCCG 1 1 1 AACCUUACCAG 0 1 1 CCUUCG 1 0 0 UCUCAG 1 0 0 CCUAACCCUUG 1 0 0 UCCAUG 1 0 1 CCAUCAUUCAG 0 1 0 UCACUG 0 1 1 CCUAAUACAUG 0 1 1 UACCUG 1 0 0 CUUAACACAUG 1 0 0 AUUCCG 0 1 0 UACCUUACCAG 0 1 0 AUCCUG 1 1 1 CAUUAG 0 1 1 UACCUCAUUAG 0 0 1 UAAUCG 1 1 1 UAACUG 1 1 1 [ CCCCCUUUUIAG 0 1 0 AUACUG 1 0 0 UAACCCUUUUG 0 0 1 UUUCCG 1 1 1 UUUCCCCUUUG 1 0 0 CUUUCG 1 0 0 (UCIUCUG 1 0 0 UCAUUG 0 1 1 ZDuodecamer AACCUUACCAAG 1 0 0 UUUUCG 0 1 1 ACUAA[CUClAAAG 1 0 0 Heptamer [CAA,CCCUUAAlUG 0 1 0 AACACCG 1 0 0 CCCUUAACUCUG 1 0 0 CAAACAG 0 1 1 UCAAAUCAUCAUG 1 1 ri CACUCCG 0 1 1 CAAUCUUACAAUG 0 1' 1 CCUACCG 1 0 0 CAACUCG 1 1 1 AUUUCUCCCUUCG 0 1' 0 CAACCUG 0 1 1 UAACACG 1 1 1 CUAAUCCCAAAAAG 1 0 0 UACAACG 1" 0 0 CACAAUG 1 0 0 UAAA[CCUCUUUlCP 1 0 0 UAAAAAG 0 1 0 {UAA,UCCAlU[CU,CI 0 1 0 G CUUCACG 1 0 0 UUCCCAG 0 1 1 AUAUACCU- 0 1 0 UUCCCUUCG CAUUCAG 0 0 1 CCAAUCCCACAAAA 0 1 0 UUCACAG 1 0 0 CUAAUCCC AUAAAP 0 0 1 ~ - - - 308 PECHMAN, LEWIS, AND WOESE INT. J. SYST.BACTERIOL, TABLE1 -Continued - Oligonucleotide Oligonucleotide v) s $ 8 8 Y Y $ Y * v; 5 - - UAACCUG 1 0 ACUCAUG 1 0 Post-transcriptionally modi- ’ledf ACCUUAG 0 0 AACUCUG 0 0 AUG 1 0 0 CAUUAAG 1 1 UACAAUG 1 0 GCCG 1 w 1 UAAUACG 1 1 AUAUCAG 1 0 CCCCG 1 1 1 AAACUUG 0 0 CAACG 1 1 ob UACCUUG 0 1 UAACAAG 1 1 1 UUAUCCG 1 0 UUCCAUG 1 0 UCACACCACG 0 1 1 AAUAUUG 1 0 UCAAAUCAUCAUG 0 0 1 CUUUCUG 0 1 j ’-Termini PU,,,UUUACG 1 0 0 pU[CUUlAUG 0 1 0 pUAUUAUG 0 0 1 3 ’-Termini AUCACCU[CCUUUlU,,, -1 1 1 ‘’ The number of copies of an oligonucleotide found in a given RNA is indicated by the numerals 0,1,2, etc. Where this number is somewhat uncertain, a range, e.g., 1-2, etc., is given. For B. subtilis and B. stearotherrnophilus, whose complete catalogs are not given herein, + and ++ denote the presence of one copy and two copies, respectively, of a given oligonucleotide in that organism; - denotes its absence. The complete catalogs for these two organisms are given elsewhere (18). * The absence of the given oligonucleotide is likely but not totally certain. ‘’ The presence of the given oligonucleotide is likely but not totally certain. This oligonucleotide occurs in B.pasteurii; however, the initial C, i.e., UCAA. , is post-transcription- ally modified in that case; see below. f’ The sequence of the given oligonucleotide is likely but not totally certain. A post-transcriptionally modified base is indicated by a superscript dot.
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