scholarly journals Identification and Distribution of New Insertion Sequences in the Genome of Alkaliphilic Bacillus halodurans C-125

2001 ◽  
Vol 183 (14) ◽  
pp. 4345-4356 ◽  
Author(s):  
Hideto Takami ◽  
Chang-Gyun Han ◽  
Yoshihiro Takaki ◽  
Eiichi Ohtsubo
Keyword(s):  
Response Regulator ◽  
Bacillus Halodurans ◽  
Insertion Sequences ◽  
Significant Similarity ◽  
New Members ◽  
Noncoding Regions ◽  
Is Elements ◽  
Atp Binding Cassette Transporter ◽  
Alkaline Conditions ◽  
Alkaliphilic Bacillus

ABSTRACT Fifteen kinds of new insertion sequences (ISs), IS641 to IS643, IS650 to IS658, IS660, IS662, and IS663, and a group II intron (Bh.Int) were identified in the 4,202,352-bp genome of alkaliphilic Bacillus halodurans C-125. Out of 120 ISs identified in the C-125 genome, 29 were truncated, indicating the occurrence of internal rearrangements of the genome. The ISs other than IS650, IS653, IS660, and IS663generated a 2- to 9-bp duplication of the target site sequence, and the ISs other than IS650, IS653, and IS657 carry 14- to 64-bp inverted repeats. Sequence analysis revealed that six kinds of ISs (IS642, IS643, IS654, IS655, IS657, and IS658) belong to a separate IS family (IS630, IS21, IS256, IS3, IS200/IS605, and IS30, respectively) as a new member. Also, IS651 and IS652 were characterized as new members of the ISL3 family. Significant similarity was found between the transposase (Tpase) sequences between IS650 and IS653 (78.2%), IS651 and IS652 (56.3%), IS656 and IS662 (71.0%), and IS660 and IS663 (44.5%), but the others showed no similarity to one another. Tpases in 28 members of IS651 in the C-125 genome were found to have become diversified. Most of the IS elements widely distributed throughout the genome were inserted in noncoding regions, although some genes, such as those coding for an ATP-binding cassette transporter/permease, a response regulator, andl-indole 2-dehydrogenase, have been mutated through the insertion of IS elements. It is evident, however, that not all IS elements have transposed and caused rearrangements of the genome in the past 17 years during which strain C-125 was subcultured under neutral and alkaline conditions.

A globin-coupled oxygen sensor from the facultatively alkaliphilic Bacillus halodurans C-125

Extremophiles ◽  
2001 ◽  
Vol 5 (5) ◽  
pp. 351-354 ◽  
Author(s):  
Shaobin Hou ◽  
Claude Belisle ◽  
Summer Lam ◽  
Mikhail Piatibratov ◽  
Victor Sivozhelezov ◽  
...  
Keyword(s):  
Oxygen Sensor ◽  
Bacillus Halodurans ◽  
Alkaliphilic Bacillus

Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125

Extremophiles ◽  
2000 ◽  
Vol 4 (4) ◽  
pp. 209-214 ◽  
Author(s):  
K. Nakasone ◽  
Noriaki Masui ◽  
Yoshihiro Takaki ◽  
Rumie Sasaki ◽  
G. Maeno ◽  
...  
Keyword(s):  
Comparative Study ◽  
Bacillus Halodurans ◽  
Alkaliphilic Bacillus ◽  
Rrn Operons

scholarly journals F1FoATP synthase a-subunit of Stenotrophomonas sp. DL18 from Indian Soda Lake, Lonar: a brief report

F1000Research ◽  
2012 ◽  
Vol 1 ◽  
pp. 62
Author(s):  
Devendra Lingojwar ◽  
Ravikant Jadhav ◽  
Kachru Gawai
Keyword(s):  
Ribosomal Rna ◽  
Molecular Basis ◽  
Soda Lake ◽  
Biotechnology Industry ◽  
Significant Similarity ◽  
Naturally Occurring ◽  
Alkaline Conditions ◽  
Lonar Lake ◽  
A Subunit ◽  
Original Habitat

Lonar Lake, an Indian Soda Lake, is well known for its biodiversity of extremophiles including alkaliphiles. Most of the molecular studies on Lonar Lake alkaliphiles are based on molecular identification by 16S ribosomal RNA along with numerous applications in the biotechnology industry. However, molecular basis of adaptation of these alkaliphiles to high alkaline conditions is incompletely understood. Attempts were made to isolate and identify alkaliphiles from their naturally occurring original habitat, i.e. Lonar Lake, India with high alkaline conditions of pH 10.5. One facultative alkaliphile, Stenotrophomonas species DL18, was studied for F1FoATP synthase a-subunit with reference to alkaliphile-specific domains. Although the a-subunit of Stenotrophomonas DL18 showed significant similarity with neutrophiles, the isolated bacterium is an alkaliphile and optimally grows at pH 10.5.

scholarly journals Frequent Transposition of Multiple Insertion Sequences in Geobacillus kaustophilus HTA426

2021 ◽  
Vol 12 ◽  
Author(s):  
Hirokazu Suzuki ◽  
Tatsunari Taketani ◽  
Misaki Tanabiki ◽  
Misaki Ohara ◽  
Jyumpei Kobayashi ◽  
...  
Keyword(s):  
Stress Responses ◽  
Sigma Factor ◽  
Elevated Temperatures ◽  
Thermophilic Bacterium ◽  
Insertion Sequences ◽  
Is Elements ◽  
Evolutionary Diversification ◽  
Growth Inhibitory ◽  
Geobacillus Kaustophilus ◽  
Mutant Genes

Geobacillus kaustophilus HTA426 is a thermophilic bacterium whose genome harbors numerous insertion sequences (IS). This study was initially conducted to generate mutant genes for thermostable T7 RNA polymerase in G. kaustophilus; however, relevant experiments unexpectedly identified that the organism transposed multiple IS elements and produced derivative cells that expressed a silent gene via transposition. The transposed elements were diverse and included members of the IS4, IS701, IS1634, and ISLre2 families. The transposition was relatively active at elevated temperatures and generated 4–9 bp of direct repeats at insertion sites. Transposition was more frequent in proliferative cells than in stationary cells but was comparable between both cells when sigX, which encodes an extra-cytoplasmic function sigma factor, was forcibly expressed. Southern blot analysis indicated that IS transposition occurred under growth inhibitory conditions by diverse stressors; however, IS transposition was not detected in cells that were cultured under growth non-inhibitory conditions. These observations suggest that G. kaustophilus enhances IS transposition via sigX-dependent stress responses when proliferative cells were prevented from active propagation. Considering Geobacillus spp. are highly adaptive bacteria that are remarkably distributed in diverse niches, it is possible that these organisms employ IS transposition for environmental adaptation via genetic diversification. Thus, this study provides new insights into adaptation strategies of Geobacillus spp. along with implications for strong codependence between mobile genetic elements and highly adaptive bacteria for stable persistence and evolutionary diversification, respectively. This is also the first report to reveal active IS elements at elevated temperatures in thermophiles and to suggest a sigma factor that governs IS transposition.

scholarly journals The three heavy-chain precursors for the inter-α-inhibitor family in mouse: new members of the multicopper oxidase protein group with differential transcription in liver and brain

1995 ◽  
Vol 306 (2) ◽  
pp. 505-512 ◽  
Author(s):  
P Chan ◽  
J L Risler ◽  
G Raguenez ◽  
J P Salier
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mouse Liver ◽  
Multicopper Oxidase ◽  
Sequence Comparisons ◽  
Significant Similarity ◽  
New Members ◽  
Protein Group ◽  
A Domains ◽  
Differential Transcription

The inter-alpha-inhibitor (I alpha I) family is comprised of the plasma protease inhibitors I alpha I, inter-alpha-like inhibitor (I alpha LI), pre-alpha-inhibitor (P alpha I) and bikunin. I alpha I, I alpha LI and P alpha I are distinct assemblies of bikunin with one of three heavy (H) chains designated H1, H2 and H3. These H chains and bikunin are respectively encoded by a set of three H genes and an alpha 1-microglobulin/bikunin precursor (AMBP) gene. All four gene products undergo maturation steps from precursor polypeptides. The full-length cDNAs for the H1-, H2- and H3-chain precursors were cloned from a mouse liver cDNA library and sequenced. Extensive searches of amino acid sequence similarities to other proteins in databanks revealed (i) a highly significant similarity of the C-terminal sequence in the three H-chain precursors to the multicopper-binding domain in the group of multicopper oxidase proteins and (ii) the presence of von Willebrand type-A domains in the mature H chains. Amino acid sequence comparisons between the three mouse H1-, H2- and H3-chain precursors and their human counterparts allowed us to appraise the timing and order of occurrence of the three H-chain genes from a shared ancestor during mammalian evolution. Owing to a multiple alignment of the six mouse and human nucleotide sequences for these H-chain precursors, a reverse transcriptase PCR assay with degenerate oligonucleotides was designed, allowing us to (i) present evidence that no mRNAs for further H genes exist in mouse liver and (ii) demonstrate a previously undescribed transcription of the H2- and H3-chain mRNAs in mouse brain, which contrasts with the expression of all four, H1, H2, H3 and AMBP, mRNAs in liver.

scholarly journals High Prevalence of Diverse Insertion Sequences within the rRNA Operons of Mycoplasma bovis

2016 ◽  
Vol 82 (21) ◽  
pp. 6386-6394 ◽  
Author(s):  
Eytan Amram ◽  
Ilya Borovok ◽  
Yaarit Nachum-Biala ◽  
Roger Ayling ◽  
Uri Lerner ◽  
...  
Keyword(s):  
Pcr Analysis ◽  
Mycoplasma Bovis ◽  
Insertion Sequences ◽  
Putative Promoter ◽  
Ribosome Synthesis ◽  
Content Type ◽  
Is Elements ◽  
Viable Cells ◽  
High Prevalence ◽  
And Function

ABSTRACTInsertion sequences (ISs) are widespread in the genome ofMycoplasma bovisstrain PG45, but no ISs were identified within its two tandemly positioned rRNA operons (rrn1andrrn2). However, characterization of therrnlocus in 70M. bovisisolates revealed the presence of ISs related to the ISMbov1(IS30family) and ISMbov4(IS4family) isomers in 35 isolates. ISs were inserted into intergenic region 1 (IGR-1) or IGR-3, which are the putative promoter regions ofrrn1andrrn2, respectively, and into IGR-5, located downstream of therrl2gene. Seven different configurations (A to G) of therrnlocus with respect to ISs were identified, including those in five annotated genomes. The transcriptional start site for the singlerrnoperon inM. bovisstrain 88127 was mapped within IGR-1, 60 bp upstream of therrsgene. Notably, only 1 nucleotide separated the direct repeat (DR) for ISMbov1and the promoter –35 element in configuration D, while in configuration F, the −35 motif was a part of the ISMbov1DR. Relative quantitative real-time (qRT) PCR analysis and growth rate comparisons detected a significant increase (P< 0.05) in the expression of therrsgenes and in the number of viable cells during log phase growth (8, 12, and 16 h) in the strains with configuration F in comparison to strains with one or tworrnoperons that did not have ISs. A high prevalence of IS elements within or close to theM. bovisrrnoperon-promoter region may reflect their important role in regulation of both ribosome synthesis and function.IMPORTANCEData presented in this study show a high prevalence of diverse ISs within theM. bovis rrnlocus resulting in intraspecies variability and diversity. Such abundance of IS elements near or within therrnlocus may offer a selective advantage toM. bovis. Moreover, the fact that expression of therrsgenes as well as the number of viable cells increased in the group of strains with IS element insertion within a putative promoter −35 sequence (configuration F) in comparison to that in strains with one or tworrnoperons that do not have ISs may serve as a basis for understanding the possible role ofM. bovisIS elements in fundamental biological processes such as regulation of ribosome synthesis and function.

Sequence analysis, cloning and over-expression of an endoxylanase from the alkaliphilic Bacillus halodurans

2005 ◽  
Vol 27 (8) ◽  
pp. 545-550 ◽  
Author(s):  
M. Alejandra Martínez ◽  
Osvaldo D. Delgado ◽  
Mario D. Baigorí ◽  
Faustino Siñeriz
Keyword(s):  
Sequence Analysis ◽  
Bacillus Halodurans ◽  
Over Expression ◽  
Alkaliphilic Bacillus

scholarly journals Novel Insertion Sequence Elements Associated with Genetic Heterogeneity and Phenotype Conversion in Ralstonia solanacearum

2000 ◽  
Vol 182 (16) ◽  
pp. 4673-4676 ◽  
Author(s):  
Eun-Lee Jeong ◽  
Jeremy N. Timmis
Keyword(s):  
Genetic Heterogeneity ◽  
Ralstonia Solanacearum ◽  
Insertion Sequence ◽  
Southern Hybridization ◽  
Insertion Sequences ◽  
Is Elements ◽  
Conversion Event ◽  
Sequence Elements ◽  
Different Strains ◽  
Insertion Sequence Elements

ABSTRACT Three insertion sequences (IS) elements were isolated from the phytopathogen Ralstonia solanacearum. Southern hybridization using these IS elements as probes revealed hybridization profiles that varied greatly between different strains of the pathogen. During a spontaneous phenotype conversion event, the promoter of thephcA gene was interrupted by one of these IS elements.

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