Genome mining and marine microbial natural products.

204 Pages·2020·17.829 MB·English

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Edited by
Kui Hong, Changsheng Zhang and Alan Dobson
Printed Edition of the Special Issue Published in Marine Drugs
www.mdpi.com/journal/marinedrugs
Genome Mining and Marine Microbial
Natural Products

Genome Mining and Marine Microbial
Natural Products
SpecialIssueEditors
KuiHong
ChangshengZhang
AlanDobson
MDPI•Basel•Beijing•Wuhan•Barcelona•Belgrade
SpecialIssueEditors
KuiHong Changsheng Zhang Alan Dobson
WuhanUniversity Chinese Academy of Sciences University College Cork
China China Ireland
EditorialOffice
MDPI
St.Alban-Anlage66
4052Basel,Switzerland
This is a reprint of articles from the Special Issue published online in the open access journal
MarineDrugs (ISSN 1660-3397) from 2017 to 2019 (available at: https://www.mdpi.com/journal/
marinedrugs/specialissues/genomemicrobe).
Forcitationpurposes,citeeacharticleindependentlyasindicatedonthearticlepageonlineandas
indicatedbelow:
LastName,A.A.; LastName,B.B.; LastName,C.C.ArticleTitle. JournalNameYear,ArticleNumber,
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ISBN978-3-03928-090-2(Pbk)
ISBN978-3-03928-091-9(PDF)
(cid:2)c 2019bytheauthors. ArticlesinthisbookareOpenAccessanddistributedundertheCreative
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publishedarticles,aslongastheauthorandpublisherareproperlycredited,whichensuresmaximum
disseminationandawiderimpactofourpublications.
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licenseCCBY-NC-ND.
Contents
AbouttheSpecialIssueEditors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Prefaceto”GenomeMiningandMarineMicrobialNaturalProducts” . . . . . . . . . . . . . . ix
Alka Choudhary, Lynn M. Naughton, Itxaso Monta´nchez, Alan D. W. Dobson and
Dilip K. Rai
Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials
Reprintedfrom:Mar.Drugs2017,15,272,doi:10.3390/md15090272 . . . . . . . . . . . . . . . . . 1
ThomasE.Smith
BiogeneticRelationshipsofBioactiveSpongeMerotriterpenoids
Reprintedfrom:Mar.Drugs2017,15,285,doi:10.3390/md15090285 . . . . . . . . . . . . . . . . . 43
NajeebAkhter,YaqinLiu,BibiNaziaAuckloo,YutongShi,KuiwuWang,JuanjuanChen,
XiaodanWuandBinWu
Stress-Driven Discovery of New Angucycline-Type Antibiotics from a Marine
StreptomycespratensisNA-ZhouS1
Reprintedfrom:Mar.Drugs2018,16,331,doi:10.3390/md16090331 . . . . . . . . . . . . . . . . . 66
PatriciaGo´mez-Villegas,JavierVigaraandRosaLeo´n
Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel
Marshlands(SWSpain)
Reprintedfrom:Mar.Drugs2018,16,332,doi:10.3390/md16090332 . . . . . . . . . . . . . . . . . 82
LiLiao,ShiyuanSu,BinZhao,ChengqiFan,JinZhang,HuirongLiandBoChen
BiosyntheticPotentialofaNovelAntarcticActinobacteriumMarisediminicolaantarcticaZS314T
RevealedbyGenomicDataMiningandPigmentCharacterization
Reprintedfrom:Mar.Drugs2019,17,388,doi:10.3390/md17070388 . . . . . . . . . . . . . . . . . 99
Wei Liu, Wenjun Zhang, Hongbo Jin, Qingbo Zhang, Yuchan Chen, Xiaodong Jiang,
GuangtaoZhang,LipingZhang,WeiminZhang,ZhigangSheandChangshengZhang
Genome Mining of Marine-Derived Streptomyces sp. SCSIO 40010 Leads to Cytotoxic New
PolycyclicTetramateMacrolactams
Reprintedfrom:Mar.Drugs2019,17,663,doi:10.3390/md17120663 . . . . . . . . . . . . . . . . . 114
LinXu,Kai-XiongYe,Wen-HuaDai,CongSun,Lian-HuaXuandBing-NanHan
Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster
DistributionsofMarineStreptomyces
Reprintedfrom:Mar.Drugs2019,17,498,doi:10.3390/md17090498 . . . . . . . . . . . . . . . . . 128
YingYin,QiangFu,WenhuiWu,MenghaoCai,XiangshanZhouandYuanxingZhang
Producing Novel Fibrinolytic Isoindolinone Derivatives in Marine Fungus
Stachybotrys longispora FG216 by the Rational Supply of Amino Compounds According to
ItsBiosynthesisPathway
Reprintedfrom:Mar.Drugs2017,15,214,doi:10.3390/md15070214 . . . . . . . . . . . . . . . . . 146
XinZhen,TingGong,Yan-HuaWen,Dao-JiangYan,Jing-JingChenandPingZhu
Chrysoxanthones A–C, Three New Xanthone–Chromanone Heterdimers from
Sponge-AssociatedPenicilliumchrysogenumHLS111TreatedwithHistoneDeacetylaseInhibitor
Reprintedfrom:Mar.Drugs2018,16,357,doi:10.3390/md16100357 . . . . . . . . . . . . . . . . . 159
v
Mengjie Zhou, Fawang Liu, Xiaoyan Yang, Jing Jin, Xin Dong, Ke-Wu Zeng, Dong Liu,
YingtaoZhang,MingMaandDonghuiYang
BacillibactinandBacillomycinAnalogueswithCytotoxicitiesagainstHumanCancerCellLines
fromMarineBacillussp.PKU-MA00093andPKU-MA00092
Reprintedfrom:Mar.Drugs2018,16,22,doi:10.3390/md16010022 . . . . . . . . . . . . . . . . . . 170
JingHou,JingLiu,LuYang,ZengzhiLiu,HuayueLi,QianChe,TianjiaoZhu,DehaiLiand
WenliLi
DiscoveryofanUnusualFattyAcidAmidefromthendgRyoGeneMutantofMarine-Derived
Streptomycesyoussoufiensis
Reprintedfrom:Mar.Drugs2019,17,12,doi:10.3390/md17010012 . . . . . . . . . . . . . . . . . . 184
vi
About the Special Issue Editors
KuiHongPh.D.,isaprofessorintheSchoolofPharmaceuticalSciences,WuhanUniversity,China.
She has studied microbiology at Wuhan University, the South China College of Tropical Crops,
Nanjing Agriculture University, and Tsinghua University, where she obtained her B.S., M.S. and
Ph.D.degrees. Since2001,herresearchhasfocusedonmarinemicrobialdrugdiscovery,especially
fromspecialmarineenvironmentssuchasmangroves,deepsea,andPolarRegions. Shehasledor
participated in the national NSFC, “863,” “973,” and the EU “FP7” and China-Thai collaborative
projects.SheisamemberoftheChineseMicrobiologySociety,ChineseBiochemistrySociety,Chinese
Pharmacological Society, and Chinese Pharmaceutical Association. She possesses 19 national and
1PCTpatentsandpublishedmorethan100internationalpapers. Sheisnowthechiefscientistof
the“NationalKeyR&DProgramofChina,”wheresheoverseesthesection“Highefficientdiscovery
andmodificationofmarinemicrobialdrugcandidate”.
Alan Dobson Ph.D., is Professor of Environmental Microbiology at University College Cork in
Ireland.HestudiedbiochemistryattheNationalUniversityofIreland,Galway,whereheobtaineda
B.Sc. in1981andaPh.D.in1985. HethenstudiedeukaryoticmolecularbiologyattheDepartment
of Molecular and Cell Biology at Baylor College of Medicine before returning to the School of
Microbiology at Cork. His group is focused on gaining a fuller understanding of how microbes
survive, grow, and interact in their various ecological niches; an approach which is fundamental
to their exploitation for biotechnological applications. He has to date published more than 190
peer-reviewedpapers.In1992,hewasawardedaFulbrightScholarshipandin1999,hereceivedthe
RoyalIrishAcademyMedalinMicrobiologyforhisworkinenvironmentalmicrobiology. In2005,
hewasawardedaD.Sc.inmicrobiologyandmolecularbiologybytheNationalUniversityofIreland
inrecognitionofhiscontributionstoresearch.In2013,hewaselectedtotheRoyalIrishAcademy.
ChangshengZhangPh.D., isaprofessorattheSouthChinaSeaInstituteofOceanology, Chinese
AcademyofSciences,China. HeobtainedaB.Sc. inbiology(ShanghaiJiaotongUniversity,China,
1994)andanM.Sc.inbiotechnology(EastChinaUniversityofScienceandTechnology,1997).In2002,
heobtainedhisPh.D.inchemicalmicrobiology(BergischeUniversityofWuppertal,Germany)with
Prof. Dr. W. Piepersberg. He carried out postdoctoral research on natural product glycosylation
studieswithJ.S.ThorsonatUniversityofWisconsin,Madison(2003–2008). In2008,hejoinedthe
South China Sea Institute of Oceanology, China Academy of Sciences. His research interest is in
marinemicrobialnaturalproductdiscoveryandbiosynthesis.Hehaspublishedmorethan90papers
inpeer-reviewedjournalssuchasScience,NatureChemicalBiology,NatureCommunications,theJournal
of American Chemical Society, and Angewandte Chemie. He is now an editorial member of Natural
ProductReports.
vii

Preface to ”Genome Mining and Marine Microbial
Natural Products”
Most of the marine microbial natural products to date have been discovered using classical
bioassay-guidedregimes. Thisprocessiscurrentlyundergoingsignificantchangesprimarilydueto
ofrapiddevelopmentsinsequencingtechnology,syntheticbiology, andbioinformatics. However,
as increasing numbers of whole-genome sequences become available, many genomes appear to
possess“silent,”orcryptic,biosyntheticgeneclusters. Theproductsoftheseappeartoberegulated
byavarietyofenvironmentalfactors,andthereforeremainlargelyundetected. Genomemininghas
becomeaveryattractivetoolfordrugdiscoveryfrommarinemicroorganisms.
Researchershavebeenusingdifferentstrategiestohelpactivatethesesilentgeneclustersfrom
microbes, includingbutnotlimitedtobioinformatictoolsforgeneandgeneclusteridentification,
geneeditingusingtheinnovativeCRISPRCas9technology,heterologousexpressionbasedstrategies,
aswellasactivationusingenvironmentalfactors.Wearegladtoseethatthesestrategiesarealsobeing
employedonmarinemicrobes,whichwillhelpinthediscoveryofmoreandmorenewcompounds.
ThisSpecialIssueprovidesanumberofinterestingexamplesofsomeoftheexcellentworkthatis
currentlybeingundertakeninthisarena.Italsohintsatthelikelihoodofmajoradvancesinthisfield
intheverynearfuture.
KuiHong,ChangshengZhang,AlanDobson
SpecialIssueEditors
ix