Abstract:
:Propionibacteria have been studied extensively since the early 1930s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content, which has previously hampered the acquisition of quality sequence data, the accurate annotation of the available genomes, and the functional characterization of genes. The recent completion of the genome sequences for several species has led researchers to reassess the taxonomical classification of the genus Propionibacterium, which has been divided into several new genres. Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-metabolic model of current and former members of the genus Propionibacterium, we demonstrate that despite sharing unique metabolic traits, these organisms have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity. This combined approach gave us new insights into the evolution of Propionibacterium metabolism and led us to propose a novel, putative ferredoxin-linked energy conservation strategy. The pan-genomic approach highlighted key differences in Propionibacterium metabolism that reflect adaptation to their environment. Results were mathematically captured in genome-scale metabolic reconstructions that can be used to further explore metabolism using metabolic modeling techniques. Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains.
journal_name
Genes (Basel)journal_title
Genesauthors
McCubbin T,Gonzalez-Garcia RA,Palfreyman RW,Stowers C,Nielsen LK,Marcellin Edoi
10.3390/genes11101115subject
Has Abstractpub_date
2020-09-23 00:00:00issue
10issn
2073-4425pii
genes11101115journal_volume
11pub_type
杂志文章相关文献
Genes文献大全abstract::Excessive fat deposition in the hepatocytes, associated with excess dietary fat intake, was related to the occurrence of fatty livers in fish. miR-101b plays the important roles in controlling lipid metabolism, but the underlying mechanism at the post-transcriptional level remains unclear. The purpose of this study is...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11080861
更新日期:2020-07-29 00:00:00
abstract::Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbr...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11030281
更新日期:2020-03-06 00:00:00
abstract::The spread of food allergens is a topic of global importance due to its impact on public health. National and International regulations ask food producers and manufacturers to declare product compositions on the label, especially in case of processed raw materials. Wheat flour (Triticum aestivum) can be contaminated b...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10030234
更新日期:2019-03-19 00:00:00
abstract::Fruit set is the earliest phase of fruit growth and represents the onset of ovary growth after successful fertilization. In parthenocarpy, fruit formation is less affected by environmental factors because it occurs in the absence of pollination and fertilization, making parthenocarpy a highly desired agronomic trait. ...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes11121441
更新日期:2020-11-30 00:00:00
abstract::Familial hypercholesterolemia (FH) is a common autosomal codominant disorder, characterized by elevated low-density lipoprotein cholesterol levels causing premature atherosclerotic cardiovascular disease. About 2900 variants of LDLR, APOB, and PCSK9 genes potentially associated with FH have been described earlier. Nev...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes12010066
更新日期:2021-01-06 00:00:00
abstract::Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes are deregulated whi...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050376
更新日期:2019-05-17 00:00:00
abstract::Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation, namely changes in tandem repeat number. Historically, tandem repeats have been designated as...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes3030461
更新日期:2012-07-26 00:00:00
abstract::This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the ...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes10020167
更新日期:2019-02-21 00:00:00
abstract::Polyspermia is an adverse phenomenon during mammalian fertilization when more than one sperm fuses with a single oocyte. The egg cell is prepared to prevent polyspermia by, among other ways, producing cortical granules (CGs), which are specialized intracellular structures containing enzymes that aim to harden the zona...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11070815
更新日期:2020-07-17 00:00:00
abstract::For medical genetic counseling, estimating the chance of a child being born with chromosome abnormality is crucially important. Cytogenetic diagnostics of parents with a balanced karyotype are a special case. Such chromosome rearrangements cannot be detected with comprehensive chromosome screening. In the current pape...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11121511
更新日期:2020-12-17 00:00:00
abstract::We set out to assess the NIH/3T3 cell proliferation activity of Arabidopsis oil body-expressed recombinant oleosin-hEGF-hEGF protein. Normally, human epidermal growth factor (hEGF) is purified through complex process, however, oleosin fusion technology provides an inexpensive and scalable platform for its purification...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11090959
更新日期:2020-08-19 00:00:00
abstract::Adiponectin plays an important role in energy homeostasis and metabolism in mammalian adipose tissue. In this study, the relationship between adiponectin gene (ADIPOQ) haplotypes and variation in growth and carcass traits in New Zealand (NZ) Romney lambs was investigated using General Linear Models (GLMs). Eight haplo...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes8060160
更新日期:2017-06-12 00:00:00
abstract::The Kelpie is a breed developed in Australia for use as a livestock herding dog. It has been proposed that the development of the breed included gene flow from the Australian Dingo (Canis dingo), a canid species present on the Australian continent for around 4000 years. The Kelpie breed is split between working and co...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050337
更新日期:2019-05-03 00:00:00
abstract::Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini, characterized by a different host range. Here w...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes2040957
更新日期:2011-11-25 00:00:00
abstract::The continuous development of new genotyping technologies requires awareness of their potential advantages and limitations concerning utility for pharmacogenomics (PGx). In this review, we provide an overview of technologies that can be applied in PGx research and clinical practice. Most commonly used are single nucle...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes11121456
更新日期:2020-12-04 00:00:00
abstract::The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9090433
更新日期:2018-08-29 00:00:00
abstract::Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) technology to study the differenc...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050396
更新日期:2019-05-22 00:00:00
abstract:BACKGROUND:Engineering apomixis in sexually reproducing plants has been long desired because of the potential to fix hybrid vigor. Validating the functionality of genes originated from apomictic species that contribute to apomixis upon transfer to sexually reproducing species is an important step. The PsASGR-BABYBOOM-l...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11091072
更新日期:2020-09-12 00:00:00
abstract::Salinity is one of the major environment factors that limits the growth of plants and the productivity of crops worldwide. It has been shown that Na+ transporters play a central role in salt tolerance and development of plants. The objective of this study was to identify Na+/H+ antiporter (NHX) genes and investigate t...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050401
更新日期:2019-05-27 00:00:00
abstract::Bone mineral density (BMD) is of concern in Prader-Willi syndrome (PWS). This study compared responses to a physical activity intervention in bone parameters and remodeling markers in youth with PWS (n = 45) and youth with non-syndromic obesity (NSO; n = 66). Measurements occurred at baseline (PRE) and after 24 weeks ...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11090984
更新日期:2020-08-24 00:00:00
abstract:BACKGROUND:HER2 (human epidermal growth factor 2)-positive breast cancer is an aggressive type of breast cancer characterized by the overexpression of the receptor-type protein tyrosine kinase HER2 or amplification of the HER2 gene. It is commonly treated by the drug trastuzumab (Herceptin), but resistance to its actio...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10080568
更新日期:2019-07-26 00:00:00
abstract::Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and th...
journal_title:Genes
pub_type: 杂志文章,评审
doi:10.3390/genes9120607
更新日期:2018-12-05 00:00:00
abstract::Histone modifications are important in regulating gene expression in eukaryotes. Of the numerous histone modifications which have been identified, acetylation is one of the best characterised and is generally associated with active genes. Histone acetylation can directly affect chromatin structure by neutralising char...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes3020320
更新日期:2012-05-29 00:00:00
abstract::In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9060306
更新日期:2018-06-19 00:00:00
abstract::n/a. ...
journal_title:Genes
pub_type: 杂志文章,已发布勘误
doi:10.3390/genes8030091
更新日期:2017-03-03 00:00:00
abstract::Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple c...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10050394
更新日期:2019-05-22 00:00:00
abstract::The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially th...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9020070
更新日期:2018-02-01 00:00:00
abstract::Sorghum is one of the world's major crops, expresses traits for resilience to climate change, and can be used for several purposes including food and clean fuels. Multiple-trait genomic prediction and selection models were implemented using genotyping-by-sequencing single nucleotide polymorphism markers and phenotypic...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes11010061
更新日期:2020-01-05 00:00:00
abstract::Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus, genome-wide identificatio...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes9030168
更新日期:2018-03-16 00:00:00
abstract::Pleurotus tuoliensis (Pt) and P. eryngii var. eryngii (Pe) are important edible mushrooms. The epigenetic and gene expression signatures characterizing major developmental transitions in these two mushrooms remain largely unknown. Here, we report global analyses of DNA methylation and gene expression in both mushrooms...
journal_title:Genes
pub_type: 杂志文章
doi:10.3390/genes10060465
更新日期:2019-06-17 00:00:00