12 research outputs found
Global genome analysis of the shikimic acid pathway reveals greater gene loss in host-associated than in free-living bacteria
<p>Abstract</p> <p>Background</p> <p>A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete shikimic acid pathway, whereas metazoans lacking this pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the pathway, we report the presence of genes encoding shikimate pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes.</p> <p>Results</p> <p>Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete shikimic acid pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-acid sequences of enzymes of the pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete shikimic acid pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic pathways.</p> <p>Conclusions</p> <p>These results challenge the conventional belief that the shikimic acid pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.</p
Identifying new biologic targets in atopic dermatitis (AD): A retrospective histologic analysis.
Measuring the Impact of Medication-Related Interventions on 30-Day Readmission Rates in a Skilled Nursing Facility
Nummular eczema of the breast following surgery and reconstruction in breast cancer patients
COVID–19-associated diffuse dermal angiomatosis managed with pentoxifylline and topical timolol
sj-docx-1-cms-10.1177_12034754241232689 – Supplemental material for Hidradenitis Suppurativa-Associated Cutaneous Squamous Cell Carcinoma in a Diverse Population
Supplemental material, sj-docx-1-cms-10.1177_12034754241232689 for Hidradenitis Suppurativa-Associated Cutaneous Squamous Cell Carcinoma in a Diverse Population by Michelle Toker, Lindsay Pattison, Pooja Srivastava, Bijal Amin, Beth N. McLellan and Steven R. Cohen in Journal of Cutaneous Medicine and Surgery</p
Cutaneous metastasis of nuclear protein of the testis carcinoma: A new presentation of a rare entity
sj-pdf-2-cms-10.1177_12034754241232689 – Supplemental material for Hidradenitis Suppurativa-Associated Cutaneous Squamous Cell Carcinoma in a Diverse Population
Supplemental material, sj-pdf-2-cms-10.1177_12034754241232689 for Hidradenitis Suppurativa-Associated Cutaneous Squamous Cell Carcinoma in a Diverse Population by Michelle Toker, Lindsay Pattison, Pooja Srivastava, Bijal Amin, Beth N. McLellan and Steven R. Cohen in Journal of Cutaneous Medicine and Surgery</p