Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

Lin, Shangrong; Haas, Stefan A.; Żemojtel, Tomasz; Xiao, Peng; Vingron, Martin; Li, Renhui

doi:10.1016/j.gene.2010.11.011

Cited by 52 publications

(41 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Comprising B10% of the entire genome, the number of insertion sequence elements of M. aeruginosa outnumbers those found in the other bloom formers, including Nostoc punctiforme (2.0%), Anabaena variabilis (1.4%) and Cylindrospermopsis raciborskii (0.9%) (Kaneko et al, 2007;Frangeul et al, 2008;Lin et al, 2011;Humbert et al, 2013). Indeed, the presence of repetitive sequences and associated transposase genes have likely made successful closure of sequenced genome sequences challenging (Frangeul et al, 2008).…”

Section: Genomic Consequences Of Nutrient Conditionsmentioning

confidence: 99%

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Steffen¹,

Dearth²,

Dill³

et al. 2014

The ISME Journal

View full text Add to dashboard Cite

The cyanobacterium Microcystis aeruginosa is a globally distributed bloom-forming organism that degrades freshwater systems around the world. Factors that drive its dispersion, diversification and success remain, however, poorly understood. To develop insight into cellular-level responses to nutrient drivers of eutrophication, RNA sequencing was coupled to a comprehensive metabolomics survey of M. aeruginosa sp. NIES 843 grown in various nutrient-reduced conditions. Transcriptomes were generated for cultures grown in nutrient-replete (with nitrate as the nitrogen (N) source), nitrogen-reduced (with nitrate, urea or ammonium acting as the N sources) and phosphate-reduced conditions. Extensive expression differences (up to 696 genes for urea-grown cells) relative to the control treatment were observed, demonstrating that the chemical variant of nitrogen available to cells affected transcriptional activity. Of particular note, a high number of transposase genes (up to 81) were significantly and reproducibly up-regulated relative to the control when grown on urea. Conversely, phosphorus (P) reduction resulted in a significant cessation in transcription of transposase genes, indicating that variation in nutrient chemistry may influence transcription of transposases and may impact the highly mosaic genomic architecture of M. aeruginosa. Corresponding metabolomes showed comparably few differences between treatments, suggesting broad changes to gene transcription are required to maintain metabolic homeostasis under nutrient reduction. The combined observations provide novel and extensive insight into the complex cellular interactions that take place in this important bloom-forming organism during variable nutrient conditions and highlight a potential unknown molecular mechanism that may drive Microcystis blooms and evolution.

show abstract

Section: Genomic Consequences Of Nutrient Conditionsmentioning

confidence: 99%

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Steffen¹,

Dearth²,

Dill³

et al. 2014

The ISME Journal

View full text Add to dashboard Cite

show abstract

“…They are found in every kingdom of life, but in bacteria, they are often more abundant in cells living in extreme environments (8)(9)(10)(11). Transposable elements are DNA sequences with defined ends that can move locus within and between genomes by means of excision and integration reactions that are independent of homologous recombination.…”

Section: Mobile Elementsmentioning

confidence: 99%

“…As a consequence, distinctive MITE-like sequences have been classed and named differently in various organisms. They are referred to as MITEs in several bacteria but also as Correia elements (CE/ NEMIS/CREE/SRE) in Neisseria; RUP, BOX, and SPRITE in Streptococcus; RPE in Rickettsia; CIR in Caulobacter and Brucella; Nezha in cyanobacteria; ISM854-1 in Microcystis; and RU-1 (ERIC/IRU), RU-2 (YPAL), or RU-3 in enterobacteria (11,35,(38)(39)(40)(41)(42)(43)(44); for a more complete list, see reference 4).…”

Section: Mobile Elementsmentioning

confidence: 99%

“…Moreover, some pairs of bacterial species were identified to be linked by a highway of gene sharing, meaning that numerous different genes were horizontally transferred between these cells (522). Cyanobacteria living in extreme environments contain more mobile elements, which increase their genome plasticity and their chances of survival (11).…”

Section: Horizontal Gene Transfer In Prokaryotesmentioning

confidence: 99%

See 1 more Smart Citation

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

336

289

View full text Add to dashboard Cite

SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

show abstract

“…This resulted in 27 800 092 reads, of which 94% was assembled with CLC bio's software version 4.7.2 into 1363 contigs with a total length of 4.9 Mb. The large number of contigs is due to many repeats and transposons, which are far more abundant in Microcystis than in most other cyanobacteria (Lin et al, 2011). This whole-genome shotgun sequencing project has been deposited at GenBank under the accession AQPY00000000.…”

Section: Genome Sequencesmentioning

confidence: 99%

Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis

et al. 2013

View full text Add to dashboard Cite

Rising CO 2 levels may act as an important selective factor on the CO 2 -concentrating mechanism (CCM) of cyanobacteria. We investigated genetic diversity in the CCM of Microcystis aeruginosa, a species producing harmful cyanobacterial blooms in many lakes worldwide. All 20 investigated Microcystis strains contained complete genes for two CO 2 uptake systems, the ATP-dependent bicarbonate uptake system BCT1 and several carbonic anhydrases (CAs). However, 12 strains lacked either the high-flux bicarbonate transporter BicA or the high-affinity bicarbonate transporter SbtA. Both genes, bicA and sbtA, were located on the same operon, and the expression of this operon is most likely regulated by an additional LysR-type transcriptional regulator (CcmR2). Strains with only a small bicA fragment clustered together in the phylogenetic tree of sbtAB, and the bicA fragments were similar in strains isolated from different continents. This indicates that a common ancestor may first have lost most of its bicA gene and subsequently spread over the world. Growth experiments showed that strains with sbtA performed better at low inorganic carbon (C i ) conditions, whereas strains with bicA performed better at high C i conditions. This offers an alternative explanation of previous competition experiments, as our results reveal that the competition at low CO 2 levels was won by a specialist with only sbtA, whereas a generalist with both bicA and sbtA won at high CO 2 levels. Hence, genetic and phenotypic variation in C i uptake systems provide Microcystis with the potential for microevolutionary adaptation to changing CO 2 conditions, with a selective advantage for bicA-containing strains in a high-CO 2 world.

show abstract

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

Cited by 52 publications

References 42 publications

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Bacterial Genome Instability

Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis

Contact Info

Product

Resources

About