Wu Enhui, Qiao Liang *
Ishami rya chimie, kaminuza ya Fudan, Shanghai 200433, Ubushinwa
Microorganism ifitanye isano rya hafi n'indwara z'abantu n'ubuzima. Nigute ushobora gusobanukirwa ibigize mikorobe n'imikorere yabyo nikibazo gikomeye kigomba kwigwa byihutirwa. Mu myaka yashize, metaproteomics yabaye uburyo bwa tekiniki bwingenzi bwo kwiga imiterere n'imikorere ya mikorobe. Nubwo bimeze bityo ariko, bitewe nuburemere nuburinganire bukabije bwikitegererezo cya mikorobe, gutunganya icyitegererezo, gukusanya amakuru ya rusange no gusesengura amakuru byabaye ibibazo bitatu bikomeye byugarije metaproteomics. Mu isesengura rya metaproteomics, akenshi birakenewe ko umuntu atezimbere uburyo butandukanye bwintangarugero hanyuma agatandukanya mikorobe zitandukanye, gukungahaza, gukuramo na lysis. Bisa na proteome yubwoko bumwe, uburyo bwo kubona amakuru ya rusange muburyo bwa metaproteomics harimo uburyo bwo kubona amakuru (DDA) nuburyo bwo kwigenga (DIA). Uburyo bwo kubona amakuru ya DIA burashobora gukusanya rwose amakuru ya peptide yicyitegererezo kandi ifite amahirwe menshi yiterambere. Nyamara, kubera ubunini bwikigereranyo cya metaproteome, isesengura ryamakuru ya DIA ryabaye ikibazo gikomeye kibuza gukwirakwiza cyane metaproteomics. Kubyerekeranye no gusesengura amakuru, intambwe yingenzi ni iyubakwa rya protein ikurikirana. Ingano nubuziranenge bwububiko ntibigira ingaruka zikomeye kumubare wamenyekanye, ahubwo binagira ingaruka kubisesengura kumoko no kurwego rwimikorere. Kugeza ubu, igipimo cya zahabu cyo kubaka metaproteome base ni protein ikurikirana ikurikirana ishingiye kuri metagenome. Muri icyo gihe, uburyo rusange bwo kuyungurura ububiko bushingiye kubushakashatsi bwerekanwe nabwo byagaragaye ko bufite agaciro gakomeye. Duhereye ku ngamba zihariye zo gusesengura amakuru, peptide ishingiye kuri DIA uburyo bwo gusesengura amakuru yafashe inzira nyamukuru. Hamwe niterambere ryokwiga byimbitse nubwenge bwubuhanga, bizateza imbere cyane ukuri, gukwirakwiza no gusesengura umuvuduko wa macroproteomic data. Kubyerekeranye no gusesengura bioinformatics yo hepfo, hateguwe urutonde rwibikoresho byo gutangaza amakuru mu myaka yashize, bishobora gukora ibisobanuro by’ibinyabuzima ku rwego rwa poroteyine, urwego rwa peptide ndetse na gene kugira ngo bibone imiterere ya mikorobe. Ugereranije nubundi buryo bwa omics, isesengura ryimikorere ya mikorobe ni ikintu cyihariye cya macroproteomics. Macroproteomics yabaye igice cyingenzi cyo gusesengura ibintu byinshi bya mikorobe, kandi iracyafite amahirwe menshi yiterambere mubijyanye n'uburebure bwimbitse, ibyiyumvo byo kumenya, hamwe nisesengura ryamakuru.
01Icyitegererezo
Kugeza ubu, tekinoroji ya metaproteomics yakoreshejwe cyane mu bushakashatsi bwa mikorobe ya kimuntu, ubutaka, ibiryo, inyanja, imyanda ikora nizindi nzego. Ugereranije nisesengura rya proteome ryubwoko bumwe, icyitegererezo cyo kugereranya metaproteome yintangarugero zitoroshye zihura nibibazo byinshi. Imiterere ya mikorobe mubyitegererezo nyabyo iragoye, urwego rwinshi rwinshi ni runini, imiterere yurukuta rwimiterere yubwoko butandukanye bwa mikorobe iratandukanye cyane, kandi ibyitegererezo akenshi birimo proteine nyinshi zakira nibindi byanduye. Kubwibyo, mu isesengura rya metaproteome, akenshi ni nkenerwa guhuza ubwoko butandukanye bwintangarugero no gufata mikorobe zitandukanye, gutungisha, gukuramo na lysis.
Gukuramo mikorobe ya mikorobe biva mubitegererezo bitandukanye bifite aho bihuriye kimwe nibitandukaniro bimwe, ariko kuri ubu harabura uburyo bumwe bwo kubanza gutunganya uburyo butandukanye bwikigereranyo cya metaproteome.
02Mass spekrometrike yo gushaka amakuru
Mu isesengura rya poroteyine ya poroteyine, imvange ya peptide nyuma yo kwitegura itandukanijwe bwa mbere mu nkingi ya chromatografique, hanyuma ikinjira muri mass spectrometer kugirango ibone amakuru nyuma ya ionisiyoneri. Bisa nubwoko bumwe bwa proteome isesengura, uburyo rusange bwo kubona amakuru muburyo bwo gusesengura macroproteome harimo uburyo bwa DDA nuburyo bwa DIA.
Hamwe nogukomeza kwisubiramo no kuvugurura ibikoresho bya spekrometrike, ibikoresho bya spekrometrike hamwe na sensibilité nini kandi ikemurwa bikoreshwa kuri metaproteome, kandi ubwimbike bwimbitse bwisesengura rya metaproteome nabwo burakomeza kunozwa. Kuva kera, urukurikirane rwibikoresho bihanitse cyane bya spekrometrike iyobowe na Orbitrap byakoreshejwe cyane muri metaproteome.
Imbonerahamwe 1 yinyandiko yumwimerere yerekana ubushakashatsi bumwe buhagarariye kuri metaproteomics kuva 2011 kugeza ubu mubijyanye nubwoko bwikitegererezo, ingamba zo gusesengura, ibikoresho bya sprometrike, uburyo bwo kugura, software isesengura, numubare wabiranga.
03Isesengura ryamakuru ya spassrometrie
3.1 Ingamba zo gusesengura amakuru ya DDA
3.1.1 Gushakisha Ububikoshingiro
3.1.2de novoingamba zikurikirana
3.2 Ingamba zo gusesengura amakuru ya DIA
04Uburyo bwihariye bwo gutondeka no gutangaza imikorere
Ibigize mikorobe kurwego rutandukanye rwa tagisi nimwe mubice byingenzi byubushakashatsi mubushakashatsi bwa mikorobe. Mu myaka ya vuba aha, hateguwe urutonde rwibikoresho byo gutangaza amoko ku rwego rwa poroteyine, urwego rwa peptide, ndetse n’urwego rwa gene kugira ngo haboneke imiterere ya mikorobe.
Intangiriro yo gutangaza imikorere ni ukugereranya intego ya poroteyine ikurikirana hamwe nububiko bwa poroteyine bukurikirana. Ukoresheje ububiko bwimikorere ya gene nka GO, COG, KEGG, amagiNOG, nibindi, isesengura ryimikorere itandukanye rishobora gukorwa kuri poroteyine zagaragajwe na macroproteomes. Ibikoresho byo gutangaza birimo Blast2GO, DAVID, KOBAS, nibindi
05 Incamake na Outlook
Microorganism igira uruhare runini mubuzima bwabantu nindwara. Mu myaka yashize, metaproteomics yabaye uburyo bwa tekiniki bwingenzi bwo kwiga imikorere ya mikorobe. Inzira yisesengura ya metaproteomics isa niy'ubwoko bumwe na bumwe bwa proteomics, ariko kubera ubunini bwibintu byubushakashatsi bwa metaproteomics, ingamba zihariye zubushakashatsi zigomba gukurikizwa muri buri ntambwe yisesengura, uhereye kubitekerezo, kwishakira amakuru kugeza kubisesengura ryamakuru. Kugeza ubu, tubikesha kunoza uburyo bwo kwitegura, guhanga udushya twinshi mu ikoranabuhanga rya spekrometrike hamwe niterambere ryihuse rya bioinformatics, metaproteomics ryateye intambwe nini muburyo bwimbitse no mubisabwa.
Muburyo bwo kubanza kuvura macroproteome ntangarugero, imiterere yicyitegererezo igomba kubanza gusuzumwa. Uburyo bwo gutandukanya ibinyabuzima na selile n’ibidukikije ni imwe mu mbogamizi zingenzi zihura na macroproteomes, kandi uburinganire hagati yo gutandukana no gutakaza mikorobe nikibazo cyihutirwa gikemurwa. Icya kabiri, gukuramo poroteyine mikorobe bigomba kuzirikana itandukaniro ryatewe nuburyo butandukanye bwa bagiteri zitandukanye. Urugero rwa Macroproteome murwego rwurwego rusaba kandi uburyo bwihariye bwo kuvura.
Kubyerekeranye nibikoresho rusange bya sprometrike, ibikoresho rusange bya sprometrometrice byanyuze mubyerekezo biva mubisumizi rusange bishingiye kubisesengura rusange bya Orbitrap nka LTQ-Orbitrap na Q Exactive kuri mass spectrometrice ishingiye kuri ion igendana nigihe cyo guhaguruka-isesengura rusange nka timsTOF Pro . TimsTOF yuruhererekane rwibikoresho hamwe na ion yimikorere yamakuru afite amakuru yukuri yo kumenya neza, kugabanuka guke, no gusubiramo neza. Buhoro buhoro babaye ibikoresho byingenzi mubice bitandukanye byubushakashatsi bisaba gutahura ibintu byinshi, nka proteome, metaproteome, na metabolome yubwoko bumwe. Birakwiye ko tumenya ko igihe kinini, urwego rwibikoresho bya spekrometrike igabanya poroteyine yimbitse yubushakashatsi bwa metaproteome. Mu bihe biri imbere, ibikoresho bya sprometrometrike hamwe nimbaraga nini nini birashobora kunoza ibyiyumvo byukuri no kumenya poroteyine muri metaproteomes.
Kugirango abantu benshi babone amakuru, nubwo uburyo bwa DIA bwo gukusanya amakuru bwakoreshejwe cyane muri proteome yubwoko bumwe, isesengura ryinshi rya macroproteome riracyakoresha uburyo bwo kubona amakuru ya DDA. Uburyo bwa DIA bwo kubona amakuru burashobora kubona byimazeyo amakuru yamakuru yintangarugero, kandi ugereranije nuburyo bwo kubona amakuru ya DDA, ifite ubushobozi bwo kubona byimazeyo amakuru ya peptide yicyitegererezo cya macroproteome. Ariko, kubera ubunini bukabije bwamakuru ya DIA, isesengura ryamakuru macroproteome ya DIA riracyafite ibibazo bikomeye. Iterambere ryubwenge bwubuhanga hamwe no kwiga byimbitse biteganijwe ko bizamura ukuri nuzuye kwisesengura ryamakuru ya DIA.
Mu isesengura ryamakuru ya metaproteomics, imwe muntambwe zingenzi nukubaka data base ikurikirana. Kubice byubushakashatsi bizwi cyane nka flora yo munda, ububiko bwa mikorobe yo munda nka IGC na HMP burashobora gukoreshwa, kandi ibisubizo byiza byo kumenyekana byagezweho. Kubindi bisobanuro byinshi bya metaproteomics, ingamba zifatika zubaka zububiko ziracyari ugushiraho icyitegererezo cyihariye cya poroteyine zikurikirana zishingiye ku makuru akurikirana ya metagenomic. Kubaturage ba mikorobe ntangarugero zifite ubunini buringaniye kandi nini nini cyane, birakenewe kongera ubujyakuzimu bwikurikiranya kugirango hongerwe kumenyekanisha amoko make, bityo tunonosore ikwirakwizwa ryububiko bwa poroteyine. Mugihe amakuru akurikirana yabuze, uburyo bwo gushakisha bushobora gukoreshwa mugutezimbere ububiko rusange. Nyamara, gushakisha itera bishobora kugira ingaruka ku kugenzura ubuziranenge bwa FDR, ibisubizo byubushakashatsi rero bigomba kugenzurwa neza. Mubyongeyeho, ikoreshwa rya moderi gakondo yo kugenzura ubuziranenge bwa FDR mugusesengura metaproteomics iracyakwiye gushishoza. Kubireba ingamba zishakisha, ingamba zo gusoma za Hybrid zishobora kunoza ubwuzuzanye bwa DIA metaproteomics. Mu myaka yashize, isomero ryerekanwe ryakozwe rishingiye ku myigire yimbitse ryerekanye imikorere isumba izindi muri proteomics ya DIA. Nyamara, metaproteome data base ikunze kuba irimo amamiriyoni ya poroteyine yinjira, bivamo igipimo kinini cyamasomero yahanuwe, ikoresha ibikoresho byinshi byo kubara, kandi bivamo umwanya munini wo gushakisha. Byongeye kandi, isano iri hagati ya poroteyine ikurikirana muri metaproteomes iratandukanye cyane, bigatuma bigorana kumenya neza niba uburyo bwo guhanura isomero ryerekana, bityo amasomero yahanuwe ntabwo yakoreshejwe cyane muri metaproteomics. Byongeye kandi, ingamba nshya za poroteyine hamwe n’ingamba zo gutangaza ibyiciro bigomba gutegurwa kugira ngo bikoreshe isesengura rya metaproteomics ya poroteyine zikurikirana cyane.
Muri make, nkubuhanga bugaragara bwa tekinoroji yubushakashatsi, tekinoroji ya metaproteomics yageze kubisubizo byubushakashatsi kandi ifite n'iterambere ryinshi.
Igihe cyo kohereza: Kanama-30-2024