Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: Presence of short rRNA corresponding to approximately the first 130 nt of the 23S rRNA in some alpha-Proteobacteria as shown by Northern hybridization of total RNA separated on a 1.2% agarose formaldehyde gel with the radioactively labeled oligonucleotide 23Sup130. Lanes: 1, E. coli JM109; 2, R. capsulatus 37b4; 3, R. capsulatus Fm65; 4, R. capsulatus Fm65 (pRK2fm1); 5, R. sphaeroides 17023; 6, R. palustris 5D; 7, R. rubrum DSM 107; 8, R. gallicum R602; 9, R. giardinii H152.

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques: Northern Blot, Hybridization, Labeling

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

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Figure Lengend Snippet: Models of potential secondary structure of helix 9 in the 23S rRNA primary transcript of the following strains (asterisks indicate sequences obtained from the data bank, the other sequences were determined in our laboratory, and EMBL accession numbers are in parentheses): A, R. rubrum DSM 107 (AJ251267); B, R. sphaeroides WS8 (AJ251261); C, R. sphaeroides 17023 (AJ251260); D, R. capsulatus B10 (AJ251256); E, R. capsulatus 37b4 (AJ251255); F, R. capsulatus DSM 938* (reference 11); G, R. palustris 5D (AJ251262); H, B. japonicum 110* (reference 17); I, B. bacilliformis KC 584* (reference 22); J, B. henselae ATCC 49882 (AJ251257); K, S. fredii MSDJ 1536 (AJ251258); L, R. giardinii H152 (AJ251263); M, R. etli CFN 42 (AJ251265); R. etli Viking I (AJ251266); O, R. gallicum R602 (AJ251259), R. leguminosarum ATCC 10004 (AJ251264). (B to F) Rhodobacter group of helices. Boxes with highly conservative base pair occupation, specific for this group, are indicated. The differences between the sequences shown in panels E and F are in boldface letters. (G to P) Rhizobium-Bradyrhizobium group of helices. Boxes with highly conservative base pair occupation, specific for this group, are indicated. In panels G and H, sequences of high similarity around the putative deletion and/or insertion site are underlined. Arrows indicate the approximate positions of the RNase III processing sites as determined by RNA fragment length estimation (Table ​(Table4).4). Arrows on the left side of the helices indicate 5′-processing sites; arrows on the right side of the helices indicate 3′-processing sites. Filled arrowheads indicate primary processing sites; empty arrowheads indicate secondary processing sites.

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques:

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: Summary of the approximate lengths of the helix 9 containing transcripts from the strains studied here and the approximate lengths of the fragments arising after in vitro cleavage of these transcripts by RNases III from R. capsulatus and E. coli a

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques: In Vitro

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: Percentage of sequence identity found by comparison of the first 30 bp of the helix 9 of 23S rRNA of various bacterial strains a

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques: Sequencing

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: GC content of helix 9 of 23S rRNA in comparison with the overall GC content of complete rrn operons or 23S rRNA

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques:

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: Percentage of in vitro-cleaved transcripts containing helix 9 of 23S rRNA using E. coli and R. capsulatus RNases III at 130 mM and 250 mM KCl a

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques: In Vitro

Journal:

Article Title: RNase III Processing of Intervening Sequences Found in Helix 9 of 23S rRNA in the Alpha Subclass of Proteobacteria

doi:

Figure Lengend Snippet: In vitro processing of transcripts containing helix 9 of 23S rRNA by R. capsulatus (Rc) and E. coli (Ec) RNase III at low and high monovalent ion concentrations. L, 130 mM KCl; H, 250 mM KCl; C, uncleaved substrate. Rp, R. palustris; Rc, R. capsulatus; Bh, B. henselae; Rhe, R. etli; Rs, R. sphaeroides; Rhgi, R. giardinii; Sf, S. fredi; Rhga, R. gallicum; Rhl, R. leguminosarum.

Article Snippet: Rp , R. palustris ; Rc , R. capsulatus ; Bh , B. henselae ; Rhe , R. etli ; Rs , R. sphaeroides ; Rhgi , R. giardinii ; Sf , S. fredi ; Rhga , R. gallicum ; Rhl , R. leguminosarum . table ft1 table-wrap mode="anchored" t5 TABLE 4 caption a7 Transcript source strain (lane nos. in Fig. ) Approximate length (no. of nt) of: Full-length transcript 5′-End fragment Internal fragment 3′-End fragment R. sphaeroides WS8 (21–25) 180 40 50 90 R. sphaeroides 17023 (56–58) 145 55 (40) – (15) 90 R. capsulatus B10 (46–50) 145 55 (40) – (15) 90 R. capsulatus 37b4 (6–10) 200 110 (40) – (70) 90 R. palustris 5D (1–5) 170 * 40 40 90 B. henselae ATCC 49882 (11–15) 160 * 40 ** 30 ** 90 ** S. fredii MSDJ 1536 (31–35) 160 40 30 90 R. giardinii H152 (26–30) 160 40 30 90 R. etli CFN 42 (16–20) 260 * 40 ** 130 (processed in fragments of 30–40 nt) 90 ** R. etli Viking I (41–45) 250 * 40 ** 120 (processed in fragments of 30–40 nt) 90 ** R. gallicum R602 (36–40) 310 * 40 ** 180 (processed further) 90 ** R. leguminosarum ATCC 10004 (51–55) 250 * 40 ** 120 ** 90 ** Open in a separate window a In some of the Rhodobacter strains, the 3′-cleavage site was used as a primary processing site, and only a small amount of the 5′ fragment is further processed at the secondary, 5′-processing site.

Techniques: In Vitro