FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2991160459> ?p ?o ?g. }

• W2991160459 abstract "ABSTRACT Rhamnose is a constituent of lipo- and capsular polysaccharides, and cell surface glycoproteins. L-rhamnose is biosynthesized by the rml or udp pathway and D-rhamnose by the gdp pathway. Disruption of its biosynthesis affects survival, colonisation, etc. Rhamnosides are commercially important in pharmaceutical and cosmetics industries. HMM profiles were used to investigate the prevalence of the three pathways in completely sequenced genomes and metagenomes. The three pathways are mutually exclusive except in Pseudomonas which has both rml and gdp pathways. The rml pathway is restricted to bacteria (42% genomes), archaea (21%) and bacteriophages, and absent in eukaryotes and other viruses. The gdp pathway is restricted to Pseudomonas and Aneurinibacillus . The udp pathway is primarily found in plants, fungi and algae, and in human faecal metagenomic samples. The rml pathway is found in >40% genomes of Actinobacteria, Bacteroidetes, Crenarchaeota, Cyanobacteria, Fusobacteria and Proteobacteria but in <20% genomes of Chlamydiae, Euryarchaeota and Tenericutes. The udp pathway is found in all genomes of Streptophyta, <=25% genomes of Ascomycota and Chordata, and none of the genomes of Arthropoda and Basidiomycota. Some genera which lack any of these pathways are Chlamydia , Helicobacter , Listeria , Mycoplasma , Pasteurella , Rickettsia and Staphylococcus . Organisms such as E. coli and Salmonella enterica showed significant strain-specific differences in the presence/absence of rhamnose pathways. Identification of rhamnose biosynthesis genes facilitates profiling their expression pattern, and in turn, better understanding the physiological role of rhamnose. Knowledge of phylogenetic distribution of biosynthesis pathways helps in fine graining the taxonomic profiling of metagenomes. AUTHOR SUMMARY In the present study, we have investigated the prevalence of rhamnose biosynthesis pathways in completely sequenced genomes and metagenomes. It is observed that the prevalence of rhamnose is highly clade specific: present in all plants but in less than half of all prokaryotes. Among chordates, only the Chinese rufous horseshoe bat has rhamnose biosynthesis pathway and this exclusive presence is quite baffling. The effect of disrupting rhamnose biosynthesis has been reported in a few prokaryotes and all these cases pointed to the essentiality of rhamnose for critical physiological processes such as survival, colonisation, etc. In this background, it is surprising that many of the prokaryotes such as Escherichia coli and Salmonella enterica show significant strain-specific differences in the presence/absence of rhamnose pathway. This study will facilitate the experimental characterization of rhamnose biosynthesis genes in organisms where this pathway has not been characterised yet, eventually leading to the elucidation of the biological role of rhamnose. Phylum-, genus-, species- and strain-level differences found with respect to presence of rhamnose biosynthesis pathway genes can be used as a tool for taxonomic profiling of metagenome samples. This study could also annotate a significant number of orphan proteins in the TrEMBL database." @default.
• W2991160459 created "2019-12-05" @default.
• W2991160459 creator A5006668020 @default.
• W2991160459 creator A5081386318 @default.
• W2991160459 date "2019-11-25" @default.
• W2991160459 modified "2023-10-17" @default.
• W2991160459 title "Highly clade-specific biosynthesis of rhamnose: present in all plants and in only 42% of prokaryotes. OnlyPseudomonasuses both D- and L-rhamnose" @default.
• W2991160459 cites W1482481751 @default.
• W2991160459 cites W1484310592 @default.
• W2991160459 cites W1572124882 @default.
• W2991160459 cites W1586017516 @default.
• W2991160459 cites W1604805669 @default.
• W2991160459 cites W1611041432 @default.
• W2991160459 cites W1941669181 @default.
• W2991160459 cites W1952785817 @default.
• W2991160459 cites W1964275733 @default.
• W2991160459 cites W1964398531 @default.
• W2991160459 cites W1971684652 @default.
• W2991160459 cites W1972610733 @default.
• W2991160459 cites W1972645668 @default.
• W2991160459 cites W1973073889 @default.
• W2991160459 cites W1977608631 @default.
• W2991160459 cites W1982998197 @default.
• W2991160459 cites W1986622235 @default.
• W2991160459 cites W1987203712 @default.
• W2991160459 cites W1992232200 @default.
• W2991160459 cites W2009921642 @default.
• W2991160459 cites W2010236879 @default.
• W2991160459 cites W2014044488 @default.
• W2991160459 cites W2014485659 @default.
• W2991160459 cites W2015905438 @default.
• W2991160459 cites W2016411536 @default.
• W2991160459 cites W2017317070 @default.
• W2991160459 cites W2025134892 @default.
• W2991160459 cites W2027529667 @default.
• W2991160459 cites W2030490424 @default.
• W2991160459 cites W2032355465 @default.
• W2991160459 cites W2035527162 @default.
• W2991160459 cites W2035691419 @default.
• W2991160459 cites W2036448942 @default.
• W2991160459 cites W2044932774 @default.
• W2991160459 cites W2054922991 @default.
• W2991160459 cites W2058433928 @default.
• W2991160459 cites W2065761900 @default.
• W2991160459 cites W2066897427 @default.
• W2991160459 cites W2069178899 @default.
• W2991160459 cites W2077739032 @default.
• W2991160459 cites W2080295051 @default.
• W2991160459 cites W2085725048 @default.
• W2991160459 cites W2087644906 @default.
• W2991160459 cites W2090037460 @default.
• W2991160459 cites W2094009696 @default.
• W2991160459 cites W2098231525 @default.
• W2991160459 cites W2102528366 @default.
• W2991160459 cites W2103017472 @default.
• W2991160459 cites W2104046482 @default.
• W2991160459 cites W2105305395 @default.
• W2991160459 cites W2108504202 @default.
• W2991160459 cites W2109570313 @default.
• W2991160459 cites W2109670638 @default.
• W2991160459 cites W2111890864 @default.
• W2991160459 cites W2112948265 @default.
• W2991160459 cites W2113246421 @default.
• W2991160459 cites W2113908179 @default.
• W2991160459 cites W2117319600 @default.
• W2991160459 cites W2117945331 @default.
• W2991160459 cites W2120057950 @default.
• W2991160459 cites W2121886331 @default.
• W2991160459 cites W2122745481 @default.
• W2991160459 cites W2122988740 @default.
• W2991160459 cites W2123113723 @default.
• W2991160459 cites W2124076845 @default.
• W2991160459 cites W2129583295 @default.
• W2991160459 cites W2130815099 @default.
• W2991160459 cites W2131420795 @default.
• W2991160459 cites W2131891756 @default.
• W2991160459 cites W2133482511 @default.
• W2991160459 cites W2134062395 @default.
• W2991160459 cites W2138194089 @default.
• W2991160459 cites W2149034211 @default.
• W2991160459 cites W2149837711 @default.
• W2991160459 cites W2156533097 @default.
• W2991160459 cites W2157122199 @default.
• W2991160459 cites W2160553490 @default.
• W2991160459 cites W2161514872 @default.
• W2991160459 cites W2166826022 @default.
• W2991160459 cites W2167896930 @default.
• W2991160459 cites W2168120282 @default.
• W2991160459 cites W2168625333 @default.
• W2991160459 cites W2169543355 @default.
• W2991160459 cites W2171728746 @default.
• W2991160459 cites W2174380698 @default.
• W2991160459 cites W2299259157 @default.
• W2991160459 cites W2412176113 @default.
• W2991160459 cites W2796034603 @default.
• W2991160459 cites W2883195299 @default.
• W2991160459 cites W2898402099 @default.
• W2991160459 cites W3136918052 @default.
• W2991160459 cites W4238110371 @default.
• W2991160459 cites W4240796863 @default.

• next