Abstract:
BACKGROUND:Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0°C and 37°C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS). RESULTS:We found expression of 2,058 transcripts in all replicates from both platforms and differential expression of 564 genes (absolute log2FC≥1, P-value<0.001) comparing the two temperatures by RNA-Seq. A total of 73 spots were differentially expressed between the two temperatures on 2D-DIGE, 25 of which were identified by MS/MS. Some proteins exhibited patterns of dispersion in the gel that are characteristic of post-translational modifications. CONCLUSIONS:Our findings suggest that the two sequencing platforms yielded similar results and that different omic approaches may be used to improve the understanding of gene expression. To adapt to low temperatures, E. antarcticum B7 expresses four of the six cold-shock proteins present in its genome. The cold-shock proteins were the most abundant in the bacterial proteome at 0°C. Some of the differentially expressed genes are required to preserve transcription and translation, while others encode proteins that contribute to the maintenance of the intracellular environment and appropriate protein folding. The results denote the complexity intrinsic to the adaptation of psychrotrophic organisms to cold environments and are based on two omic approaches. They also unveil the lifestyle of a bacterial species isolated in Antarctica.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Dall'Agnol HP,Baraúna RA,de Sá PH,Ramos RT,Nóbrega F,Nunes CI,das Graças DA,Carneiro AR,Santos DM,Pimenta AM,Carepo MS,Azevedo V,Pellizari VH,Schneider MP,Silva Adoi
10.1186/1471-2164-15-986subject
Has Abstractpub_date
2014-11-18 00:00:00pages
986issn
1471-2164pii
1471-2164-15-986journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-555
更新日期:2010-10-11 00:00:00
abstract:BACKGROUND:Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06917-z
更新日期:2020-07-22 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00
abstract:BACKGROUND:Recent research has revealed that polymorphic behavioral strategies shape intra-and interspecific interactions and contribute to fitness in many animal species. A better understanding of the proximate mechanisms underlying these behavioral syndromes will enhance our grasp this phenomenon. Spiders in the genu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6172-5
更新日期:2019-11-22 00:00:00
abstract:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4656-3
更新日期:2018-04-16 00:00:00
abstract:BACKGROUND:Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the org...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1121
更新日期:2014-12-16 00:00:00
abstract:BACKGROUND:The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo at the transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal (IC40) concentrations of the drug to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-358
更新日期:2008-07-30 00:00:00
abstract:BACKGROUND:Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy langu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1394-7
更新日期:2015-03-17 00:00:00
abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2474-z
更新日期:2016-02-29 00:00:00
abstract:BACKGROUND:Infectious salmon anemia virus (ISAV) causes a multisystemic disease responsible for severe losses in salmon aquaculture. Better understanding of factors that explain variations in resistance between individuals and families is essential for development of strategies for disease control. To approach this, we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-179
更新日期:2008-04-18 00:00:00
abstract:BACKGROUND:Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6097-z
更新日期:2019-10-12 00:00:00
abstract:BACKGROUND:Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-169
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still un...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3403-x
更新日期:2017-01-05 00:00:00
abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5791-1
更新日期:2019-05-28 00:00:00
abstract:BACKGROUND:Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3729-z
更新日期:2017-05-04 00:00:00
abstract:BACKGROUND:GLV-1h68 is an attenuated recombinant vaccinia virus (VACV) that selectively colonizes established human xenografts inducing their complete regression. RESULTS:Here, we explored xenograft/VACV/host interactions in vivo adopting organism-specific expression arrays and tumor cell/VACV in vitro comparing VACV ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-301
更新日期:2009-07-07 00:00:00
abstract:BACKGROUND:Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-318
更新日期:2014-04-28 00:00:00
abstract:BACKGROUND:Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure to low nonfreezing temperatures. As a subtropical evergreen broadleaf plant, oil-tea camellia demons...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3570-4
更新日期:2017-02-28 00:00:00
abstract:BACKGROUND:Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2397-8
更新日期:2016-03-10 00:00:00
abstract:BACKGROUND:Early maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting of 355 upland cotton germplasm accessions was genotyped using the specific-locus amplified fragm...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2875-z
更新日期:2016-08-30 00:00:00
abstract:BACKGROUND:Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the express...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-725
更新日期:2013-10-22 00:00:00
abstract:BACKGROUND:Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. RESULTS:Here, we present eight new Ptr isolate g...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4680-3
更新日期:2018-04-23 00:00:00
abstract:BACKGROUND:The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3946-5
更新日期:2017-07-21 00:00:00
abstract:BACKGROUND:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced chan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07164-y
更新日期:2020-11-04 00:00:00
abstract:BACKGROUND:Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5418-y
更新日期:2019-01-16 00:00:00
abstract:BACKGROUND:Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and functio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06942-y
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) w...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4063-1
更新日期:2017-08-23 00:00:00
abstract:BACKGROUND:An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2965-y
更新日期:2016-08-15 00:00:00
abstract:BACKGROUND:Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. Therefore, the present study was conducted to determine if different levels of vegetable and fish oils ca...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4099-2
更新日期:2017-09-08 00:00:00
abstract:BACKGROUND:Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA meth...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-698
更新日期:2014-08-20 00:00:00