A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution

Author(s):  
Xue-Qiang Zeng ◽  
Guo-Zheng Li ◽  
Jack Y. Yang ◽  
Mary Qu Yang
Keyword(s):  
2019 ◽  
Vol 85 (12) ◽  
Author(s):  
Xinyu Lu ◽  
Weiwei Wang ◽  
Lige Zhang ◽  
Haiyang Hu ◽  
Ping Xu ◽  
...  

ABSTRACTN,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified asMethylobacteriumsp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation byMethylobacterium.IMPORTANCEDMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader,Methylobacteriumsp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes ofMethylobacterium.


2002 ◽  
Vol 363 (3) ◽  
pp. 437-447 ◽  
Author(s):  
Laurent KREMER ◽  
Sudagar S. GURCHA ◽  
Pablo BIFANI ◽  
Paul G. HITCHEN ◽  
Alain BAULARD ◽  
...  

Phosphatidyl-myo-inositol mannosides (PIMs), lipomannan (LM) and lipoarabinomannan (LAM) are an important class of bacterial factors termed modulins that are found in tuberculosis and leprosy. Although their structures are well established, little is known with respect to the molecular aspects of the biosynthetic machinery involved in the synthesis of these glycolipids. On the basis of sequence similarity to other glycosyltransferases and our previous studies defining an α-mannosyltransferase from Mycobacterium tuberculosis, named PimB [Schaeffer, Khoo, Besra, Chatterjee, Brennan, Belisle and Inamine (1999) J. Biol. Chem. 274, 31625–31631], which catalysed the formation of triacyl (Ac3)-PIM2 (i.e. the dimannoside), we have identified a related gene from M. tuberculosis CDC1551, now designated pimC. The use of a cell-free assay containing GDP-[14C]mannose, amphomycin and membranes from Myobacterium smegmatis overexpressing PimC led to the synthesis of a new alkali-labile PIM product. Fast-atom-bombardment MS established the identity of the new enzymically synthesized product as Ac3PIM3 (i.e. the trimannoside). The results indicate that pimC encodes an α-mannosyltransferase involved in Ac3PIM3 biosynthesis. However, inactivation of pimC in Myobacterium bovis Bacille Calmette—Guérin (BCG) did not affect the production of higher PIMs, LM and LAM when compared with wild-type M. bovis BCG, suggesting the existence of redundant gene(s) or an alternate pathway that may compensate for this PimC deficiency. Further analyses, which compared the distribution of pimC in a panel of M. tuberculosis strains, revealed that pimC was present in only 22% of the clinical isolates examined.


2006 ◽  
Vol 33 (8) ◽  
pp. 757 ◽  
Author(s):  
Frank Sainsbury ◽  
Alexander D. Tattersall ◽  
Michael J. Ambrose ◽  
Lynda Turner ◽  
T. H. Noel Ellis ◽  
...  

The genomes of several legume species contain two Phantastica-like genes. Previous studies on leaf development have found that Phantastica confers leaf blade adaxial identity in plant species with simple leaves and leaflet adaxial identity in pea (Pisum sativum L.), a legume with compound leaves. Previous characterisation of the phantastica mutant of pea, crispa, showed it had radialised leaflets, but stipules were not radialised. This suggested either that mutation of a second redundant gene was required for radialisation of stipules, or, that a null mutation was required. Previously characterised crispa mutants may not have exhibited radialised stipules because they were weak alleles. In this work we show that pea has a second Phantastica-like gene, which lies on a different chromosome to Crispa. The second gene was found to be a pseudogene in several genotypes of pea, therefore it would not have a role in conferring stipule adaxial identity. A new deletion mutant, crispa-4 was identified. The mutant has radialised stipules and leaflets, showing that Crispa confers adaxial identity on both these organs in pea. The nucleotide sequence data reported here are in the EMBL and GenBank Nucleotide Databases under the accession numbers DQ486060 (JI 2822), DQ486061 (JI 15), DQ486062 (JI 281) and DQ486063 (JI 399).


2014 ◽  
Vol 6 (10) ◽  
pp. 2654-2664 ◽  
Author(s):  
Myriam Badawi ◽  
Isabelle Giraud ◽  
Fabrice Vavre ◽  
Pierre Grève ◽  
Richard Cordaux

2002 ◽  
Vol 18 (6) ◽  
pp. 863-870 ◽  
Author(s):  
Nishank Trivedi ◽  
Jared Bischof ◽  
Steve Davis ◽  
Kevin Pedretti ◽  
Todd E. Scheetz ◽  
...  

1978 ◽  
Vol 34 (3) ◽  
pp. 332-333 ◽  
Author(s):  
F. García-Olmedo ◽  
P. Carbonero ◽  
C. Aragoncillo ◽  
G. Salcedo

2020 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares

Abstract Background: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.


2008 ◽  
Vol 9 (Suppl 6) ◽  
pp. S8 ◽  
Author(s):  
Xue-Qiang Zeng ◽  
Guo-Zheng Li ◽  
Jack Y Yang ◽  
Mary Yang ◽  
Geng-Feng Wu

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