Intragenomic variation in the internal transcribed spacer regions between 16S-23S rRNA genes among the three copies of Sinorhizobium fredii strains

Yuichi Saeki, Hiroko Oguro, Isao Akagi, Takeo Yamakawa, Akihiro Yamamoto

Research output: Contribution to journalArticle

Abstract

The soybean-nodulating Sinorhizobium fredii strain has been reported to possess three copies of rRNA gene operons. In the present study, we investigated the diversity of the 16S-23S rDNA internal transcribed spacer (ITS) regions of S. fredii strains. Based on the sequences of the ITS regions, we divided the sequences of the S. fredii strains into two groups, type A and type B. A dot-matrix analysis indicated that the region flanked by tRNA-Ile and tRNA-Ala is longer in type A than in type B, whereas type B sequences possess longer regions upstream of tRNA-Ile and downstream of tRNA-Ala than those of the type A sequence. Restriction fragment length polymorphism of polymerase chain reaction product (PCR-RFLP) of the ITS region in the cloned plasmids as templates could reconstruct the PCR-RFLP pattern from the total DNA as a template. The results of Southern hybridization using the insert sequence between tRNA-Ile and tRNA-Ala in type A as a probe indicated differences in the copy numbers of the type A ITS regions among the strains tested. These results indicated that S. fredii strains possess the type A and type B sequences of the ITS regions at ratios of 3:0, 2:1, 1:2 or 0:3. These S. fredii strains may be useful biological materials for the study of intraspecific variations.

Original languageEnglish
Pages (from-to)627-633
Number of pages7
JournalSoil Science and Plant Nutrition
Volume55
Issue number5
DOIs
Publication statusPublished - Oct 1 2009

Fingerprint

Sinorhizobium fredii
internal transcribed spacers
ribosomal RNA
gene
restriction fragment length polymorphism
genes
operon
intraspecific variation
Southern blotting
plasmid
plasmids
polymerase chain reaction
soybean
soybeans
polymorphism
probe
DNA
matrix

All Science Journal Classification (ASJC) codes

  • Soil Science
  • Plant Science

Cite this

Intragenomic variation in the internal transcribed spacer regions between 16S-23S rRNA genes among the three copies of Sinorhizobium fredii strains. / Saeki, Yuichi; Oguro, Hiroko; Akagi, Isao; Yamakawa, Takeo; Yamamoto, Akihiro.

In: Soil Science and Plant Nutrition, Vol. 55, No. 5, 01.10.2009, p. 627-633.

Research output: Contribution to journalArticle

@article{97355c74569a4026afd4e3a292d8233f,
title = "Intragenomic variation in the internal transcribed spacer regions between 16S-23S rRNA genes among the three copies of Sinorhizobium fredii strains",
abstract = "The soybean-nodulating Sinorhizobium fredii strain has been reported to possess three copies of rRNA gene operons. In the present study, we investigated the diversity of the 16S-23S rDNA internal transcribed spacer (ITS) regions of S. fredii strains. Based on the sequences of the ITS regions, we divided the sequences of the S. fredii strains into two groups, type A and type B. A dot-matrix analysis indicated that the region flanked by tRNA-Ile and tRNA-Ala is longer in type A than in type B, whereas type B sequences possess longer regions upstream of tRNA-Ile and downstream of tRNA-Ala than those of the type A sequence. Restriction fragment length polymorphism of polymerase chain reaction product (PCR-RFLP) of the ITS region in the cloned plasmids as templates could reconstruct the PCR-RFLP pattern from the total DNA as a template. The results of Southern hybridization using the insert sequence between tRNA-Ile and tRNA-Ala in type A as a probe indicated differences in the copy numbers of the type A ITS regions among the strains tested. These results indicated that S. fredii strains possess the type A and type B sequences of the ITS regions at ratios of 3:0, 2:1, 1:2 or 0:3. These S. fredii strains may be useful biological materials for the study of intraspecific variations.",
author = "Yuichi Saeki and Hiroko Oguro and Isao Akagi and Takeo Yamakawa and Akihiro Yamamoto",
year = "2009",
month = "10",
day = "1",
doi = "10.1111/j.1747-0765.2009.00399.x",
language = "English",
volume = "55",
pages = "627--633",
journal = "Soil Science and Plant Nutrition",
issn = "0038-0768",
publisher = "Taylor and Francis Ltd.",
number = "5",

}

TY - JOUR

T1 - Intragenomic variation in the internal transcribed spacer regions between 16S-23S rRNA genes among the three copies of Sinorhizobium fredii strains

AU - Saeki, Yuichi

AU - Oguro, Hiroko

AU - Akagi, Isao

AU - Yamakawa, Takeo

AU - Yamamoto, Akihiro

PY - 2009/10/1

Y1 - 2009/10/1

N2 - The soybean-nodulating Sinorhizobium fredii strain has been reported to possess three copies of rRNA gene operons. In the present study, we investigated the diversity of the 16S-23S rDNA internal transcribed spacer (ITS) regions of S. fredii strains. Based on the sequences of the ITS regions, we divided the sequences of the S. fredii strains into two groups, type A and type B. A dot-matrix analysis indicated that the region flanked by tRNA-Ile and tRNA-Ala is longer in type A than in type B, whereas type B sequences possess longer regions upstream of tRNA-Ile and downstream of tRNA-Ala than those of the type A sequence. Restriction fragment length polymorphism of polymerase chain reaction product (PCR-RFLP) of the ITS region in the cloned plasmids as templates could reconstruct the PCR-RFLP pattern from the total DNA as a template. The results of Southern hybridization using the insert sequence between tRNA-Ile and tRNA-Ala in type A as a probe indicated differences in the copy numbers of the type A ITS regions among the strains tested. These results indicated that S. fredii strains possess the type A and type B sequences of the ITS regions at ratios of 3:0, 2:1, 1:2 or 0:3. These S. fredii strains may be useful biological materials for the study of intraspecific variations.

AB - The soybean-nodulating Sinorhizobium fredii strain has been reported to possess three copies of rRNA gene operons. In the present study, we investigated the diversity of the 16S-23S rDNA internal transcribed spacer (ITS) regions of S. fredii strains. Based on the sequences of the ITS regions, we divided the sequences of the S. fredii strains into two groups, type A and type B. A dot-matrix analysis indicated that the region flanked by tRNA-Ile and tRNA-Ala is longer in type A than in type B, whereas type B sequences possess longer regions upstream of tRNA-Ile and downstream of tRNA-Ala than those of the type A sequence. Restriction fragment length polymorphism of polymerase chain reaction product (PCR-RFLP) of the ITS region in the cloned plasmids as templates could reconstruct the PCR-RFLP pattern from the total DNA as a template. The results of Southern hybridization using the insert sequence between tRNA-Ile and tRNA-Ala in type A as a probe indicated differences in the copy numbers of the type A ITS regions among the strains tested. These results indicated that S. fredii strains possess the type A and type B sequences of the ITS regions at ratios of 3:0, 2:1, 1:2 or 0:3. These S. fredii strains may be useful biological materials for the study of intraspecific variations.

UR - http://www.scopus.com/inward/record.url?scp=70349506846&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349506846&partnerID=8YFLogxK

U2 - 10.1111/j.1747-0765.2009.00399.x

DO - 10.1111/j.1747-0765.2009.00399.x

M3 - Article

AN - SCOPUS:70349506846

VL - 55

SP - 627

EP - 633

JO - Soil Science and Plant Nutrition

JF - Soil Science and Plant Nutrition

SN - 0038-0768

IS - 5

ER -