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1. Out for a RiPP: challenges and advances in genome mining of ribosomal peptides from fungi

Author:
Simon C. Kessler; Yit-Heng Chooi
Source:
Natural product reports 2022 v.39 no.2 pp. 222-230
ISSN:
1460-4752
Subject:
multigene family,   etc   ; biosynthesis; fungi; peptides;     Show all 4 Subjects
Abstract:
... Covering up to June 2021 Ribosomally synthesized and post-translationally modified peptides (RiPPs) from fungi are an underexplored class of natural products, despite their propensity for diverse bioactivities and unique structural features. Surveys of fungal genomes for biosynthetic gene clusters encoding RiPPs have been limited in their scope due to our incomplete understanding of fungal RiPP bi ...
DOI:
10.1039/d1np00048a

2. Plant metabolic gene clusters in the multi-omics era

Author:
Chuansong Zhan; Shuangqian Shen; Chenkun Yang; Zhenhua Liu; Alisdair R. Fernie; Ian A. Graham; Jie Luo
Source:
Trends in plant science 2022 v.27 no.10 pp. 981-1001
ISSN:
1360-1385
Subject:
multigene family,   etc   ; evolution; metabolism; multiomics;     Show all 4 Subjects
Abstract:
... Secondary metabolism in plants gives rise to a vast array of small-molecule natural products. The discovery of operon-like gene clusters in plants has provided a new perspective on the evolution of specialized metabolism and the opportunity to rapidly advance the metabolic engineering of natural product production. Here, we review historical aspects of the study of plant metabolic gene clusters as ...
DOI:
10.1016/j.tplants.2022.03.002

3. Plant biosynthetic gene clusters in the context of metabolic evolution

Author:
Samuel J. Smit; Benjamin R. Lichman
Source:
Natural product reports 2022 v.39 no.7 pp. 1465-1482
ISSN:
1460-4752
Subject:
multigene family,   etc   ; biosynthesis; epigenetics; evolution; metabolites;     Show all 5 Subjects
Abstract:
... Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for spec ...
DOI:
10.1039/d2np00005a

4. Excision and integration of unconventional circularizable structures involving the erm(B) gene in enterococci

Author:
Xinxin Shan; Hong Yao; Stefan Schwarz; Dexi Li; Xin-Sheng Li; Xiang-Dang Du
Source:
Veterinary microbiology 2022 v.273 pp. 109542
ISSN:
0378-1135
Subject:
multigene family,   etc   ; antibiotic resistance; databases; excision; plasmids; transposases;     Show all 6 Subjects
Abstract:
... Traditionally, insertion sequences (ISs) play a major role in disseminating antimicrobial resistance genes (ARGs) in bacteria through transposition and translocation, forming regions that contain multiple ARGs flanked by single or multiple copies of IS. In addition, unconventional circularizable structures (UCSs), lacking recombinase genes but being surrounded by directly repeated sequences (DRs) ...
DOI:
10.1016/j.vetmic.2022.109542

5. Total Synthesis and Biosynthesis of Cyclodepsipeptide Cochinmicin I

Author:
Romina Schnegotzki; Vincent Wiebach; Marina Sánchez-Hidalgo; Marcel Tietzmann; Andreas B. zur Bonsen; Olga Genilloud; Roderich D. Süssmuth
Source:
Organic letters 2022 v.24 no.12 pp. 2344-2348
ISSN:
1523-7052
Subject:
multigene family,   etc   ; antagonists; biosynthesis; endothelin receptors; nonribosomal peptides;     Show all 5 Subjects
Abstract:
... Phenylglycines are building blocks of many non-ribosomally synthesized peptides. The dihydroxyphenylglycine-containing cyclodepsipeptide cochinmicin I exhibits endothelin receptor antagonist activity. Therefore, it represents an interesting and synthetically challenging molecule because of the racemization-prone nature of dihydroxyphenylglycine. We present the total synthesis of cochinmicin I and ...
DOI:
10.1021/acs.orglett.2c00525

6. Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis

Author:
Oksana Bilyk; Gabriel S. Oliveira; Rafaela M. de Angelo; Michell O. Almeida; Kathia Maria Honório; Finian J. Leeper; Marcio V. B. Dias; Peter F. Leadlay
Source:
Journal of the American Chemical Society 2022 v.144 no.32 pp. 14555-14563
ISSN:
1520-5126
Subject:
multigene family,   etc   ; biosynthesis; catalytic activity; metabolites; mutation; oligomycin; stereospecificity;     Show all 7 Subjects
Abstract:
... A key step in the biosynthesis of numerous polyketides is the stereospecific formation of a spiroacetal (spiroketal). We report here that spiroacetal formation in the biosynthesis of the macrocyclic polyketides ossamycin and oligomycin involves catalysis by a novel spiroacetal cyclase. OssO from the ossamycin biosynthetic gene cluster (BGC) is homologous to OlmO, the product of an unannotated gene ...
DOI:
10.1021/jacs.2c03313

7. Crossregulation of rapamycin and elaiophylin biosynthesis by RapH in Streptomyces rapamycinicus

Author:
Wenyan He; Wenfang Wang; Jiaxiang Ma; Guosong Zheng; Andrei A. Zimin; Weihong Jiang; Jinzhong Tian; Yinhua Lu
Source:
Applied microbiology and biotechnology 2022 v.106 no.5-6 pp. 2147-2159
ISSN:
0175-7598
Subject:
multigene family,   etc   ; Streptomyces; biosynthesis; biotechnology; lysine; microbiology; polyketides; rapamycin;     Show all 8 Subjects
Abstract:
... Rapamycin is an important macrocyclic antibiotic produced by Streptomyces rapamycinicus. In the rapamycin biosynthetic gene cluster (BGC), there are up to five regulatory genes, which have been shown to play important roles in the regulation of rapamycin biosynthesis. Here, we demonstrated that the rapamycin BGC-situated LAL family regulator RapH co-ordinately regulated the biosynthesis of both ra ...
DOI:
10.1007/s00253-022-11847-9

8. Early expression of the aflatoxin gene cluster in Aspergillus nomiae isolated from Brazil nut

Author:
T.A. Reis; S.M. Tralamazza; E. Coelho; P. Zorzete; D.I.T. Fávaro; B. Corrêa
Source:
Toxicon 2022 v.209 pp. 36-42
ISSN:
0041-0101
Subject:
multigene family,   etc   ; Aspergillus; Brazil nuts; biosynthesis; carcinogenicity; metabolites; Amazonia; Brazil;     Show all 8 Subjects
Abstract:
... Aspergillus nomiae is the most important contaminant in Brazil nut due to its high incidence in these nuts and its strong production of carcinogenic metabolites: aflatoxins (AF). Aflatoxin biosynthesis pathway in A. nomiae is poorly studied. Thus, in present investigation, aflatoxin production and gene cluster (aflC, aflQ, aflU, and aflX) expression profile were evaluated on two strains of A. nomi ...
DOI:
10.1016/j.toxicon.2022.01.008

9. Metabolic Blockade-Based Genome Mining Reveals Lipochain-Linked Dihydro-β-alanine Synthetases Involved in Autucedine Biosynthesis

Author:
Huaran Zhang; Chunyan Zhang; Qinglian Li; Junying Ma; Jianhua Ju
Source:
Organic letters 2022 v.24 no.30 pp. 5535-5540
ISSN:
1523-7052
Subject:
multigene family,   etc   ; Streptomyces olivaceus; biosynthesis; gene silencing; ligases; lipopeptides; skeleton;     Show all 7 Subjects
Abstract:
... Continuously mining the Streptomyces olivaceus SCSIO T05 genome leads to the identification of new lipopeptides (autucedines A–C), constituting members of the 10th skeleton isolated from this strain. The corresponding biosynthetic gene cluster (aut) was verified by heterogeneous expression, and another two analogues (autucedines D and E) were isolated from the heterogeneous expression strain. Gene ...
DOI:
10.1021/acs.orglett.2c01957

10. Structure and Candidate Biosynthetic Gene Cluster of a Manumycin-Type Metabolite from Salinispora pacifica

Author:
Gabriel Castro-Falcón; Kaitlin E. Creamer; Alexander B. Chase; Min Cheol Kim; Douglas Sweeney; Evgenia Glukhov; William Fenical; Paul R. Jensen
Source:
Journal of natural products 2022 v.85 no.4 pp. 980-986
ISSN:
1520-6025
Subject:
multigene family,   etc   ; Actinobacteria; bioinformatics; biosynthesis; circular dichroism spectroscopy; metabolites; models;     Show all 7 Subjects
Abstract:
... A new manumycin-type natural product named pacificamide (1) and its candidate biosynthetic gene cluster (pac) were discovered from the marine actinobacterium Salinispora pacifica CNT-855. The structure of the compound was determined using NMR, electronic circular dichroism, and bioinformatic predictions. The pac gene cluster is unique to S. pacifica and found in only two of the 119 Salinispora gen ...
DOI:
10.1021/acs.jnatprod.1c01117

11. Characterization of the Tellurite-Resistance Properties and Identification of the Core Function Genes for Tellurite Resistance in Pseudomonas citronellolis SJTE-3

Author:
Wanli Peng; Yanqiu Wang; Yali Fu; Zixin Deng; Shuangjun Lin; Rubing Liang
Source:
Microorganisms 2022 v.10 no.1 pp. -
ISSN:
2076-2607
Subject:
multigene family,   etc   ; Pseudomonas citronellolis; cell growth; pathogenicity; plasmids; tellurium; toxicity;     Show all 7 Subjects
Abstract:
... Tellurite is highly toxic to bacteria and commonly used in the clinical screening for pathogens; it is speculated that there is a potential relationship between tellurite resistance and bacterial pathogenicity. Until now, the core function genes of tellurite resistance and their characteristics are still obscure. Pseudomonas citronellolis SJTE-3 was found able to resist high concentrations of tell ...
DOI:
10.3390/microorganisms10010095

12. Regulation of maltocin synthesis in Stenotrophomonas maltophilia by positive and negative regulators

Author:
Wen Sun; Xiongwei Liang; Chaoyang Zhu; Ying Xu; Yuchi Ding; Yu-Ping Huang
Source:
Research in microbiology 2022 v.173 no.6-7 pp. 103956
ISSN:
0923-2508
Subject:
multigene family,   etc   ; Stenotrophomonas maltophilia; bacteriocins; bacteriophages; mitomycin; research; transcription (genetics);     Show all 7 Subjects
Abstract:
... Maltocin P28, produced by Stenotrophomonas maltophilia P28, is an R-type phage tail-like bacteriocin (PTLB). Its gene cluster consists of 23 putative genes, including nine nonstructural genes and fourteen structural genes. In this work, three nonstructural genes, mpsA, mpsH and mpsR, were found to encode transcriptional regulators to control maltocin P28 synthesis. MpsA activated the transcription ...
DOI:
10.1016/j.resmic.2022.103956

13. Third-generation sequencing: A novel tool detects complex variants in the α-thalassemia gene

Author:
Ju Long; Lei Sun; Feifei Gong; Chenghong Zhang; Aiping Mao; Yulin Lu; Jiaqi Li; Enqi Liu
Source:
Gene 2022 v.822 pp. 146332
ISSN:
0378-1119
Subject:
multigene family,   etc   ; DNA; analytical kits; genetic analysis; hematology; mutation; thalassemia; China;     Show all 8 Subjects
Abstract:
... Thalassemia is a monogenic disorder with a high carrier rate in the southern region of China. Most laboratories currently follow the protocol of testing hematologic indicators in individuals with positive hematologic indicators and then using the hot-spot mutation test kit. A novel thalassemia gene test is performed if there is a mismatch between the hematology and hot-spot mutation test results. ...
DOI:
10.1016/j.gene.2022.146332

14. pyRSD‐CoEv: A python package for selective sweep detection and co‐evolutionary gene cluster identification

Author:
Xingxing Zhu; Haoyu Zhang; Qianzi Tang
Source:
Animal genetics 2022 v.53 no.1 pp. 161-165
ISSN:
0268-9146
Subject:
multigene family,   etc   ; Internet; animal genetics; coevolution; computer software; genomics; homozygosity; phenotype;     Show all 8 Subjects
Abstract:
... Genes undergo distinct selective sweeps, and also interact and coevolve, forming the bases of complex phenotypic traits. Therefore, the identification of genes that coevolve or are under artificial selective sweeps is of great importance. However, previous computational methods have been designed for either populations of closely related breeds or individuals of distinct species. Approaches intend ...
DOI:
10.1111/age.13151

15. Biosynthesis of Tasikamides via Pathway Coupling and Diazonium-Mediated Hydrazone Formation

Author:
Guang-Lei Ma; Hartono Candra; Li Mei Pang; Juan Xiong; Yichen Ding; Hoa Thi Tran; Zhen Jie Low; Hong Ye; Min Liu; Jie Zheng; Mingliang Fang; Bin Cao; Zhao-Xun Liang
Source:
Journal of the American Chemical Society 2022 v.144 no.4 pp. 1622-1633
ISSN:
1520-5126
Subject:
multigene family,   etc   ; Lewis acids; biosynthesis; diazonium compounds; hydrazones; moieties; nonribosomal peptides;     Show all 7 Subjects
Abstract:
... Naturally occurring hydrazones are rare despite the ubiquitous usage of synthetic hydrazones in the preparation of organic compounds and functional materials. In this study, we discovered a family of novel microbial metabolites (tasikamides) that share a unique cyclic pentapeptide scaffold. Surprisingly, tasikamides A–C (1–3) contain a hydrazone group (C═N─N) that joins the cyclic peptide scaffold ...
DOI:
10.1021/jacs.1c10369

16. Discovery and Characterization of Rubrinodin Provide Clues into the Evolution of Lasso Peptides

Author:
Huanhuan Xiu; Mengjiao Wang; Christopher D. Fage; Yile He; Xiaogang Niu; Meng Han; Fei Li; Xiaoping An; Huahao Fan; Lihua Song; Guojun Zheng; Shaozhou Zhu; Yigang Tong
Source:
Biochemistry 2022 v.61 no.7 pp. 595-607
ISSN:
1520-4995
Subject:
multigene family,   etc   ; ABC transporters; Proteobacteria; bioinformatics; biosynthesis; evolution; peptides; thermal stability;     Show all 8 Subjects
Abstract:
... Lasso peptides are unique natural products that comprise a class of ribosomally synthesized and post-translationally modified peptides. Their defining three-dimensional structure is a lariat knot, in which the C-terminal tail is threaded through a macrolactam ring formed between the N-terminal amino group and an Asp or Glu side chain (i.e., an isopeptide bond). Recent genome mining strategies have ...
DOI:
10.1021/acs.biochem.2c00029

17. Sophorolipids bioproduction in the yeast Starmerella bombicola: Current trends and perspectives

Author:
Muneer Ahmed Qazi; Qinhong Wang; Zongjie Dai
Source:
Bioresource technology 2022 v.346 pp. 126593
ISSN:
0960-8524
Subject:
multigene family,   etc   ; Starmerella bombicola; biodegradability; biosurfactants; biosynthesis; sophorolipids; technology; toxicity; yeasts;     Show all 9 Subjects
Abstract:
... Sophorolipids are highly active green surfactants (glycolipid biosurfactants) getting tremendous appreciation worldwide due to their low toxicity, biodegradability, broad spectrum of applications, and significant biotechnological potential. Sophorolipids are mainly produced by an oleaginous budding yeast Starmerella bombicola using low-cost substrates. Therefore, the recent state-of-art literature ...
DOI:
10.1016/j.biortech.2021.126593

18. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing

Author:
Fan Jiang; Ai-Ping Mao; Yin-Yin Liu; Feng-Zhi Liu; Yan-Lin Li; Jian Li; Jian-Ying Zhou; Xue-Wei Tang; Ai-Ping Ju; Fa-Tao Li; Jun-Hui Wan; Lian-Dong Zuo; Dong-Zhi Li
Source:
Gene 2022 v.825 pp. 146438
ISSN:
0378-1119
Subject:
multigene family,   etc   ; gene duplication; genotype; phenotype; quantitative polymerase chain reaction; thalassemia;     Show all 6 Subjects
Abstract:
... Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PC ...
DOI:
10.1016/j.gene.2022.146438

19. Evolution of mitochondrial and nuclear genomes in Pennatulacea

Author:
Raissa I Hogan; Kevin Hopkins; Andrew J. Wheeler; Chris Yesson; A. Louise Allcock
Source:
Molecular phylogenetics and evolution 2022 pp. 107630
ISSN:
1055-7903
Subject:
multigene family,   etc   ; Pennatulacea; data collection; gene order; mitochondria; mitochondrial genome; monophyly;     Show all 7 Subjects
Abstract:
... We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders a ...
DOI:
10.1016/j.ympev.2022.107630

20. Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae

Author:
Xiakena Xiaokaiti; Yasuyuki Hashiguchi; Hidetoshi Ota; Yoshinori Kumazawa
Source:
Genes 2022 v.13 no.8 pp. -
ISSN:
2073-4425
Subject:
multigene family,   etc   ; Elapidae; mitochondrial genome; models; nanopores; phylogeny; replication origin; snakes;     Show all 8 Subjects
Abstract:
... Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem rep ...
DOI:
10.3390/genes13081470