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Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus
KTH, School of Biotechnology (BIO).ORCID iD: 0000-0002-3627-6899
2005 (English)Doctoral thesis, comprehensive summary (Other scientific)
Place, publisher, year, edition, pages
Stockholm: KTH , 2005. , 47 p.
Keyword [en]
Biotechnology, microarray, Sulfolobus, gene expression, archaea, mRNA decay, genome evolution
Keyword [sv]
Bioteknik
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-142ISBN: 91-7283-979-1 (print)OAI: oai:DiVA.org:kth-142DiVA: diva2:7284
Public defence
2005-03-11, Sal D1, Lindstedtsvägen 17, Stockholm, 10:00
Opponent
Supervisors
Note
QC 20100830Available from: 2005-03-03 Created: 2005-03-03 Last updated: 2010-08-30Bibliographically approved
List of papers
1. Dual-genome primer design for construction of DNA microarrays
Open this publication in new window or tab >>Dual-genome primer design for construction of DNA microarrays
2005 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 3, 325-332 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

Keyword
sulfolobus-solfataricus, gene, coexpression, initiation
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14479 (URN)10.1093/bioinformatics/bti001 (DOI)000226605700007 ()2-s2.0-13844264518 (Scopus ID)
Note
QC 20100830Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
2. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination
Open this publication in new window or tab >>Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination
Show others...
2004 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 18, 7046-7051 p.Article in journal (Refereed) Published
Abstract [en]

Chromosome replication origins were mapped in vivo in the two hyperthermophilic archaea, Sulfolobus acidocaidarius and Sulfolobus solfataricus, by using microarray-based marker frequency analysis. Bidirectional replication was found to be initiated in near synchrony from three separate sites in both organisms. Two of the three replication origins in each species were located in the vicinity of a cdc6/orc1 replication initiation gene, whereas no known replication-associated gene could be identified near the third origin in either organism. In contrast to initiation, replication termination occurred asynchronously, such that certain replication forks continued to progress for >40 min after the others had terminated. In each species, all replication forks advanced at similar DNA polymerization rates; this was found to be an order of magnitude below that displayed by Escherichia coli and thus closer to eukaryotic elongation rates. In S. acidocaidarius, a region containing short regularly spaced repeats was found to hybridize aberrantly, as compared to the rest of the chromosome, raising the possibility of a centromere-like function.

Keyword
thermophilic archaea, dna, genus, acidocaldarius, temperature
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-23389 (URN)10.1073/pnas.0400656101 (DOI)000221265000039 ()2-s2.0-2342468069 (Scopus ID)
Note
QC 20100830Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2017-12-12Bibliographically approved
3. Early replicating ridge-like domains in archaeal chromosomes
Open this publication in new window or tab >>Early replicating ridge-like domains in archaeal chromosomes
(English)Manuscript (preprint) (Other academic)
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-24240 (URN)
Note
QC 20100830Available from: 2010-08-30 Created: 2010-08-30 Last updated: 2010-08-30Bibliographically approved
4. Global analysis of mRNA stability in the archaeon Sulfolobus
Open this publication in new window or tab >>Global analysis of mRNA stability in the archaeon Sulfolobus
Show others...
2006 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 10, R99- p.Article in journal (Refereed) Published
Abstract [en]

Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.

Keyword
genome-wide analysis, gene-expression, escherichia-coli, half-lives, saccharomyces-cerevisiae, translation initiation, protein families, dna microarrays, single-gene, decay
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-16175 (URN)10.1186/gb-2006-7-10-r99 (DOI)000242516200017 ()2-s2.0-33947414462 (Scopus ID)
Note
QC 20100830Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved

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